32 Human Secreted Proteins

ABSTRACT

The present invention relates to novel human secreted proteins and isolated nucleic acids containing the coding regions of the genes encoding such proteins. Also provided are vectors, host cells, antibodies, and recombinant methods for producing human secreted proteins. The invention further relates to diagnostic and therapeutic methods useful for diagnosing and treating disorders related to these novel human secreted proteins.

This application is a continuation of U.S. application Ser. No.11/366,001, filed Mar, 2, 2006, which is a divisional of U.S.application Ser. No. 11/226,657, filed Sep. 15, 2005, which is adivisional of U.S. application Ser. No. 10/062,831, filed Feb. 5, 2002(now U.S. Pat. No. 7,001,992, issued Feb. 21, 2006), which is adivisional of U.S. application Ser. No. 09/690,454, filed Oct. 18, 2000(now U.S. Pat. No. 6,531,447, issued Mar. 11, 2003), which is acontinuation of U.S. application Ser. No. 09/189,144, filed Nov. 10,1998 (now abandoned), which is a continuation-in-part of InternationalApplication No. PCT/US98/10868, filed May 28, 1998, which claims benefitunder 35 U.S.C. §119(e) of U.S. Provisional Applications: 60/044,039;60/048,093; 60/048,190; 60/050,935; 60/048,101; 60/048,356 (each filedMay 30, 1997); and, 60/056,250; 60/056,296; 60/056,293 (each filed Aug.29, 1997), each of which is incorporated by reference herein in itsentirety.

FIELD OF THE INVENTION Statement Under 37 C.F.R. §1.77(b))(5)

This application refers to a “Sequence Listing” listed below, which isprovided as a text document. The document is entitled“PZ006P1C1D3C1_SeqListing.text” (187,246 bytes, created Jun. 19, 2007)and is hereby incorporated by reference in its entirety herein.

This invention relates to newly identified polynucleotides and thepolypeptides encoded by these polynucleotides, uses of suchpolynucleotides and polypeptides, and their production.

BACKGROUND OF THE INVENTION

Unlike bacterium, which exist as a single compartment surrounded by amembrane, human cells and other eucaryotes are subdivided by membranesinto many functionally distinct compartments. Each membrane-boundedcompartment, or organelle, contains different proteins essential for thefunction of the organelle. The cell uses “sorting signals,” which areamino acid motifs located within the protein, to target proteins toparticular cellular organelles.

One type of sorting signal, called a signal sequence, a signal peptide,or a leader sequence, directs a class of proteins to an organelle calledthe endoplasmic reticulum (ER). The ER separates the membrane-boundedproteins from all other types of proteins. Once localized to the ER,both groups of proteins can be further directed to another organellecalled the Golgi apparatus. Here, the Golgi distributes the proteins tovesicles, including secretory vesicles, the cell membrane, lysosomes,and the other organelles.

Proteins targeted to the ER by a signal sequence can be released intothe extracellular space as a secreted protein. For example, vesiclescontaining secreted proteins can fuse with the cell membrane and releasetheir contents into the extracellular space—a process called exocytosis.Exocytosis can occur constitutively or after receipt of a triggeringsignal. In the latter case, the proteins are stored in secretoryvesicles (or secretory granules) until exocytosis is triggered.Similarly, proteins residing on the cell membrane can also be secretedinto the extracellular space by proteolytic cleavage of a “linker”holding the protein to the membrane.

Despite the great progress made in recent years, only a small number ofgenes encoding human secreted proteins have been identified. Thesesecreted proteins include the commercially valuable human insulin,interferon, Factor VIII, human growth hormone, tissue plasminogenactivator, and erythropoeitin. Thus, in light of the pervasive role ofsecreted proteins in human physiology, a need exists for identifying andcharacterizing novel human secreted proteins and the genes that encodethem. This knowledge will allow one to detect, to treat, and to preventmedical disorders by using secreted proteins or the genes that encodethem.

SUMMARY OF THE INVENTION

The present invention relates to novel polynucleotides and the encodedpolypeptides. Moreover, the present invention relates to vectors, hostcells, antibodies, and recombinant methods for producing thepolypeptides and polynucleotides. Also provided are diagnostic methodsfor detecting disorders related to the polypeptides, and therapeuticmethods for treating such disorders. The invention further relates toscreening methods for identifying binding partners of the polypeptides.

DETAILED DESCRIPTION DEFINITIONS

The following definitions are provided to facilitate understanding ofcertain terms used throughout this specification.

In the present invention, “isolated” refers to material removed from itsoriginal environment (e.g., the natural environment if it is naturallyoccurring), and thus is altered “by the hand of man” from its naturalstate. For example, an isolated polynucleotide could be part of a vectoror a composition of matter, or could be contained within a cell, andstill be “isolated” because that vector, composition of matter, orparticular cell is not the original environment of the polynucleotide.

In the present invention, a “secreted” protein refers to those proteinscapable of being directed to the ER, secretory vesicles, or theextracellular space as a result of a signal sequence, as well as thoseproteins released into the extracellular space without necessarilycontaining a signal sequence. If the secreted protein is released intothe extracellular space, the secreted protein can undergo extracellularprocessing to produce a “mature” protein. Release into the extracellularspace can occur by many mechanisms, including exocytosis and proteolyticcleavage.

As used herein, a “polynucleotide” refers to a molecule having a nucleicacid sequence contained in SEQ ID NO:X or the cDNA contained within theclone deposited with the ATCC. For example, the polynucleotide cancontain the nucleotide sequence of the full length cDNA sequence,including the 5′ and 3′ untranslated sequences, the coding region, withor without the signal sequence, the secreted protein coding region, aswell as fragments, epitopes, domains, and variants of the nucleic acidsequence. Moreover, as used herein, a “polypeptide” refers to a moleculehaving the translated amino acid sequence generated from thepolynucleotide as broadly defined.

In the present invention, the full length sequence identified as SEQ IDNO:X was often generated by overlapping sequences contained in multipleclones (contig analysis). A representative clone containing all or mostof the sequence for SEQ ID NO:X was deposited with the American TypeCulture Collection (“ATCC”). As shown in Table 1, each clone isidentified by a cDNA Clone ID (Identifier) and the ATCC Deposit Number.The ATCC is located at 10801 University Boulevard, Manassas, Va.20110-2209, USA. The ATCC deposit was made pursuant to the terms of theBudapest Treaty on the international recognition of the deposit ofmicroorganisms for purposes of patent procedure.

A “polynucleotide” of the present invention also includes thosepolynucleotides capable of hybridizing, under stringent hybridizationconditions, to sequences contained in SEQ ID NO:X, the complementthereof, or the cDNA within the clone deposited with the ATCC.“Stringent hybridization conditions” refers to an overnight incubationat 42° C. in a solution comprising 50% formamide, 5×SSC (750 mM NaCl, 75mM sodium citrate), 50 mM sodium phosphate (pH 7.6), 5× Denhardt'ssolution, 10% dextran sulfate, and 20 μg/ml denatured, sheared salmonsperm DNA, followed by washing the filters in 0.1×SSC at about 65° C.

Also contemplated are nucleic acid molecules that hybridize to thepolynucleotides of the present invention at lower stringencyhybridization conditions. Changes in the stringency of hybridization andsignal detection are primarily accomplished through the manipulation offormamide concentration (lower percentages of formamide result inlowered stringency); salt conditions, or temperature. For example, lowerstringency conditions include an overnight incubation at 37° C. in asolution comprising 6× SSPE (20× SSPE=3M NaCl; 0.2M NaH₂PO₄; 0.02M EDTA,pH 7.4), 0.5% SDS, 30% formamide, 100 ug/ml salmon sperm blocking DNA;followed by washes at 50° C. with 1× SSPE, 0.1% SDS. In addition, toachieve even lower stringency, washes performed following stringenthybridization can be done at higher salt concentrations (e.g. 5×SSC).

Note that variations in the above conditions may be accomplished throughthe inclusion and/or substitution of alternate blocking reagents used tosuppress background in hybridization experiments. Typical blockingreagents include Denhardt's reagent, BLOTTO, heparin, denatured salmonsperm DNA, and commercially available proprietary formulations. Theinclusion of specific blocking reagents may require modification of thehybridization conditions described above, due to problems withcompatibility.

Of course, a polynucleotide which hybridizes only to polyA+ sequences(such as any 3′ terminal polyA+ tract of a cDNA shown in the sequencelisting), or to a complementary stretch of T (or U) residues, would notbe included in the definition of “polynucleotide,” since such apolynucleotide would hybridize to any nucleic acid molecule containing apoly (A) stretch or the complement thereof (e.g., practically anydouble-stranded cDNA clone).

The polynucleotide of the present invention can be composed of anypolyribonucleotide or polydeoxribonucleotide, which may be unmodifiedRNA or DNA or modified RNA or DNA. For example, polynucleotides can becomposed of single- and double-stranded DNA, DNA that is a mixture ofsingle- and double-stranded regions, single- and double-stranded RNA,and RNA that is mixture of single- and double-stranded regions, hybridmolecules comprising DNA and RNA that may be single-stranded or, moretypically, double-stranded or a mixture of single- and double-strandedregions. In addition, the polynucleotide can be composed oftriple-stranded regions comprising RNA or DNA or both RNA and DNA. Apolynucleotide may also contain one or more modified bases or DNA or RNAbackbones modified for stability or for other reasons. “Modified” basesinclude, for example, tritylated bases and unusual bases such asinosine. A variety of modifications can be made to DNA and RNA; thus,“polynucleotide” embraces chemically, enzymatically, or metabolicallymodified forms.

The polypeptide of the present invention can be composed of amino acidsjoined to each other by peptide bonds or modified peptide bonds, i.e.,peptide isosteres, and may contain amino acids other than the 20gene-encoded amino acids. The polypeptides may be modified by eithernatural processes, such as posttranslational processing, or by chemicalmodification techniques which are well known in the art. Suchmodifications are well described in basic texts and in more detailedmonographs, as well as in a voluminous research literature.Modifications can occur anywhere in a polypeptide, including the peptidebackbone, the amino acid side-chains and the amino or carboxyl termini.It will be appreciated that the same type of modification may be presentin the same or varying degrees at several sites in a given polypeptide.Also, a given polypeptide may contain many types of modifications.Polypeptides may be branched, for example, as a result ofubiquitination, and they may be cyclic, with or without branching.Cyclic, branched, and branched cyclic polypeptides may result fromposttranslation natural processes or may be made by synthetic methods.Modifications include acetylation, acylation, ADP-ribosylation,amidation, covalent attachment of flavin, covalent attachment of a hememoiety, covalent attachment of a nucleotide or nucleotide derivative,covalent attachment of a lipid or lipid derivative, covalent attachmentof phosphotidylinositol, cross-linking, cyclization, disulfide bondformation, demethylation, formation of covalent cross-links, formationof cysteine, formation of pyroglutamate, formylation,gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation,iodination, methylation, myristoylation, oxidation, pegylation,proteolytic processing, phosphorylation, prenylation, racemization,selenoylation, sulfation, transfer-RNA mediated addition of amino acidsto proteins such as arginylation, and ubiquitination. (See, forinstance, PROTEINS—STRUCTURE AND MOLECULAR PROPERTIES, 2nd Ed., T. E.Creighton, W. H. Freeman and Company, New York (1993); POSTTRANSLATIONALCOVALENT MODIFICATION OF PROTEINS, B. C. Johnson, Ed., Academic Press,New York, pgs. 1-12 (1983); Seifter et al., Meth Enzymol 182:626-646(1990); Rattan et al., Ann NY Acad Sci 663:48-62 (1992).)

“SEQ ID NO:X” refers to a polynucleotide sequence while “SEQ ID NO:Y”refers to a polypeptide sequence, both sequences identified by aninteger specified in Table 1.

“A polypeptide having biological activity” refers to polypeptidesexhibiting activity similar, but not necessarily identical to, anactivity of a polypeptide of the present invention, including matureforms, as measured in a particular biological assay, with or withoutdose dependency. In the case where dose dependency does exist, it neednot be identical to that of the polypeptide, but rather substantiallysimilar to the dose-dependence in a given activity as compared to thepolypeptide of the present invention (i.e., the candidate polypeptidewill exhibit greater activity or not more than about 25-fold less and,preferably, not more than about tenfold less activity, and mostpreferably, not more than about three-fold less activity relative to thepolypeptide of the present invention.)

Polynucleotides and Polypeptides of the Invention

Features of Protein Encoded by Gene No: 1

This gene maps to chromosome 3 and therefore polynucleotides of thepresent invention can be used in linkage analysis as a marker forchromosome 3.

This gene is expressed in several fetal tissues including brain, liver,and lung, and to a lesser extent, in adult tissues, particularly skin.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, developmental, neural,hepatic, or pulmonary disorders, particularly cancers of the abovesystem and tissues. Similarly, polypeptides and antibodies directed tothese polypeptides are useful in providing immunological probes fordifferential identification of the tissue(s) or cell type(s). For anumber of disorders of the above tissues or cells, particularly of thecentral nervous system, hepatic system, and hepatic system, expressionof this gene at significantly higher or lower levels may be routinelydetected in certain tissues or cell types (e.g. brain, cancerous andwounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine,synovial fluid or spinal fluid) or another tissue or cell sample takenfrom an individual having such a disorder, relative to the standard geneexpression level, i.e., the expression level in healthy tissue or bodilyfluid from an individual not having the disorder.

The tissue distribution indicates that polynucleotides and polypeptidescorresponding to this gene are useful for serving as a target for avariety of blocking agents, as it is likely to be involved in thepromotion of a variety of cancers. Furthermore, polynucleotides andpolypeptides corresponding to this gene are useful for the diagnosis andtreatment of cancer and other proliferative disorders. Expression withinembryonic tissue and other cellular sources marked by proliferatingcells indicates that this protein may play a role in the regulation ofcellular division. Additionally, the expression in hematopoietic cellsand tissues indicates that this protein may play a role in theproliferation, differentiation, and/or survival of hematopoietic celllineages. In such an event, this gene may be useful in the treatment oflymphoproliferative disorders, and in the maintenance anddifferentiation of various hematopoietic lineages from earlyhematopoietic stem and committed progenitor cells. Similarly, embryonicdevelopment also involves decisions involving cell differentiationand/or apoptosis in pattern formation. Thus this protein may also beinvolved in apoptosis or tissue differentiation and could again beuseful in cancer therapy. Protein, as well as, antibodies directedagainst the protein may show utility as a tumor marker and/orimmunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:11 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 1155 of SEQID NO:11, b is an integer of 15 to 1169, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:11, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 2

In specific embodiments, the polypeptides of the invention comprise thesequence:MSVPAFIDISEEDQAAELRAYLKSKGAEISEENSEGGLHVDLAQIIEACDVCLKEDDKDVESVMNSVVSLLLILEPDKQEALIESLCEKLVKFREGERPSLRLQLLSNLFHGMDKNTPVRYTVYCSLIKVAASCGAIQYIPTELDQVRKWISDWNLTTEKKHTLLRLLYEALVDCKKSDAASKVMVELLGSYTEDNASQARVDAHRCIVRALKDPNAFLFDHLLTLKPVKFLEGELIHDLLTIFVSAKLASYVKFYQNNKDFIDSLGLLHEQNMAKMRLLTFMGMAVENKEISFDTMQQELQIGADDVEAFVIDAVRTKMVYCKIDQTQRKVVVSHSTHRTFGKQQWQQLYDTLNAWKQNLNKVKNSLLSLSDT (SEQ ID NO:83), MSVPAFIDISEED (SEQ ID NO:84),QAAELRAYLKSKGAE (SEQ ID NO:85), ISEENSEGGLHVDLAQI (SEQ ID NO:86),IEACDVCLKEDDKDVESV (SEQ ID NO:87), VARPSSLFRSAWSCEW (SEQ ID NO:88),LRLQLLSNLFHG (SEQ ID NO:89), KDVESVMNSVVSLLLIL (SEQ ID NO:90),DAASKVMVELLGSYTEDNASQARVDA (SEQ ID NO:91), KMRLLTFMGMAVENKEIS (SEQ IDNO:93), and/or VEAFVIDAVR (SEQ ID NO:92). Polynucleotides encoding thesepolypeptides are also encompassed by the invention. The translationproduct of this gene shares homology with the Homo sapiens GA17 protein(gb accession number AF064603). The gene encoding the disclosed cDNA isthought to reside on the X chromosome. Accordingly, polynucleotidesrelated to this invention are useful as a marker in linkage analysis forthe X chromosome.

This gene is expressed primarily in bone, and to a lesser extent, inbrain, lung, T-cells, muscle, skin, testis, spleen and macrophages.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, skeletal, neural, orhematopoietic disorders, particularly bone cancer, osteoarthritis,autoimmune diseases. Similarly, polypeptides and antibodies directed tothese polypeptides are useful in providing immunological probes fordifferential identification of the tissue(s) or cell type(s). For anumber of disorders of the above tissues or cells, particularly of theimmune system and skeletal system, expression of this gene atsignificantly higher or lower levels may be routinely detected incertain tissues or cell types (e.g. bone, brain, lung, testis, andcancerous and wounded tissues) or bodily fluids (e.g., lymph, pulmonarysurfactant or sputum, serum, plasma, urine, synovial fluid or spinalfluid) or another tissue or cell sample taken from an individual havingsuch a disorder, relative to the standard gene expression level, i.e.,the expression level in healthy tissue or bodily fluid from anindividual not having the disorder.

Preferred epitopes include those comprising a sequence shown in SEQ IDNO:48 as residues: Arg-31 to Ser-37, Met-50 to Val-56, Glu-80 to Trp-87,Thr-94 to His-99, Tyr-129 to Ser-135, Tyr-193 to Phe-199, Ser-274 toGln-285, Ala-293 to Lys-302.

The tissue distribution in bone and immune cells and tissues indicatesthat polynucleotides and polypeptides corresponding to this gene areuseful for the diagnosis and/or treatment of skeletal and hematopoieticdisorders. Elevated levels of expression of this gene product in bonesuggest that it may be useful in influencing bone mass in suchconditions as osteoporosis, or in the stimulation or growth of bone,cartilage, and/or tendons, for example. More generally, as evidenced byexpression in T-cells and spleen, this gene may play a role in thesurvival, proliferation, and/or differentiation of hematopoietic cellsin general, and may be of use in augmentation of the numbers of stemcells and committed progenitors. Expression of this gene product inmacrophage also indicates that it may play a role in mediating responsesto infection and controlling immunological responses, such as those thatoccur during immune surveillance. Protein, as well as, antibodiesdirected against the protein may show utility as a tumor marker and/orimmunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:12 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 1296 of SEQID NO:12, b is an integer of 15 to 1310, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:12, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 3

The translation product of this gene shares sequence homology withvarious kinases. The closest homolog is the mouse TIF1 which is aconserved nuclear protein. TIF1 enhances RXR and RAR AF-2 in yeast andinteracts in a ligand-dependent manner with several nuclear receptors inyeast and mammalian cells, as well as in vitro. Remarkably, theseinteractions require the amino acids constituting the AF-2 activatingdomain conserved in all active NRs. Moreover, the estrogen receptor (ER)AF-2 antagonist hydroxytamoxifen cannot promote ER-TIF1 interaction.TIF1, which contains several conserved domains found in transcriptionalregulatory proteins, may be a mediator of ligand-dependent AF-2.Interestingly, the TIF1 N-terminal moiety is fused to B-raf in the mouseoncoprotein T18. One embodiment of this gene comprises polypeptides ofthe following amino acid sequence:MEAVPEGDWFCTVCLAQQVEGEFTQKPGFPKRGQKRKSGYSLNFSEGDGRRRRVLLRGRESPAAGPRYSEEGLSPSKRRRLSMRNHHSDLTFCEIILMEMESHDAAWPFLEPVNPRLVSGYRRIIKNPMDFSTMRERLLRGGYTSSEEFAADALLVFDNCQTFNEDDSEVGKAGHIMRRFFESRWEEFYQGKQANL (SEQ ID NO:94),MEAVPEGDWFCTVCLAQQVE (SEQ ID NO:95), GEFTQKPGFPKRGQKRKSGYS (SEQ IDNO:96), LNFSEGDGRRRRVLLRGRESP (SEQ ID NO:97), AAGPRYSEEGLSPSKRRRLS (SEQID NO:98), MRNHHSDLTFCEIILMEMESH (SEQ ID NO:99), DAAWPFLEPVNPRLVSGYRR(SEQ ID NO:100), IIKNPMDFSTMRERLLRGGYT (SEQ ID NO:101),SSEEFAADALLVFDNCQTFNE (SEQ ID NO:102), DDSEVGKAGHIMRRFFE (SEQ IDNO:103), and/or SRWEEFYQGKQANL (SEQ ID NO:104). An additional embodimentis the polynucleotides encoding these polypeptides.

This gene is expressed primarily in activated T-cells, and to a lesserextent, in testes and brain.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, immune, reproductive,or neural disorders, particularly autoimmune diseases, AIDS, leukemias,and cancers. Similarly, polypeptides and antibodies directed to thesepolypeptides are useful in providing immunological probes fordifferential identification of the tissue(s) or cell type(s). For anumber of disorders of the above tissues or cells, particularly of theimmune, reproductive, or neural systems, expression of this gene atsignificantly higher or lower levels may be routinely detected incertain tissues or cell types (e.g. immune, neural, reproductive, andcancerous and wounded tissues) or bodily fluids (e.g., lymph, serum,plasma, urine, synovial fluid or spinal fluid) or another tissue or cellsample taken from an individual having such a disorder, relative to thestandard gene expression level, i.e., the expression level in healthytissue or bodily fluid from an individual not having the disorder.

Preferred epitopes include those comprising a sequence shown in SEQ IDNO:49 as residues: Ala-31 to Glu-36.

The tissue distribution in activated T-cells, combined with the homologyto TIF indicates that polynucleotides and polypeptides corresponding tothis gene are useful for modulation of nuclear receptor and ligandinteraction in various immune disorders. Furthermore, the secretedprotein can also be used to determine biological activity, to raiseantibodies, as tissue markers, to isolate cognate ligands or receptors,to identify agents that modulate their interactions and as nutritionalsupplements. It may also have a very wide range of biologicalactivities. Typical of these are cytokine, cellproliferation/differentiation modulating activity or induction of othercytokines; immunostimulating/immunosuppressant activities (e.g. fortreating human immunodeficiency virus infection, cancer, autoimmunediseases and allergy); regulation of hematopoiesis (e.g. for treatinganaemia or as adjunct to chemotherapy); stimulation or growth of bone,cartilage, tendons, ligaments and/or nerves (e.g. for treating wounds,stimulation of follicle stimulating hormone (for control of fertility);chemotactic and chemokinetic activities (e.g. for treating infections,tumors); hemostatic or thrombolytic activity (e.g. for treatinghaemophilia, cardiac infarction etc.); anti-inflammatory activity (e.g.for treating septic shock, Crohn's disease); as antimicrobials; fortreating psoriasis or other hyperproliferative diseases; for regulationof metabolism, and behaviour. Also contemplated is the use of thecorresponding nucleic acid in gene therapy procedures. Protein, as wellas, antibodies directed against the protein may show utility as a tumormarker and/or immunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:13 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 1125 of SEQID NO:13, b is an integer of 15 to 1139, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:13, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 4

This gene maps to chromosome 11. Accordingly, polynucleotides of theinvention can be used in linkage analysis as a marker for chromosome 11.In specific embodiments, the polypeptides of the invention comprise thesequence: MSEIYLRCQDEQQYARWMAGCRLASKGRTMADSSY (SEQ ID NO:105),LVAPRFQRKFKAKQLTPRILEAHQNVAQLSLAEAQLRFIQAWQSL (SEQ ID NO:106),VGDVVKTWRFSNMRQWNVNWDIR (SEQ ID NO:107), EEIDCTEEEMMVFAALQYHINKLSQS (SEQID NO:108), and/or EEIDCTEEEMMVFAALQYHINKLSQS (SEQ ID NO:109).Polynucleotides encoding these polypeptides are also encompassed by theinvention.

This gene is expressed primarily in white blood cell types includingmonocytes, T-cells, neutrophils, and to a lesser extent, in umbilicalvein and liver.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, various diseases ofthe immune system including AIDS, immunodeficency diseases, andautoimmune disorders, in addition to hepatic and developmentaldisorders. Similarly, polypeptides and antibodies directed to thesepolypeptides are useful in providing immunological probes fordifferential identification of the tissue(s) or cell type(s). For anumber of disorders of the above tissues or cells, particularly of theimmune or hepatic system, expression of this gene at significantlyhigher or lower levels may be routinely detected in certain tissues orcell types (e.g. immune, hepatic, developmental, and cancerous andwounded tissues) or bodily fluids (e.g., lymph, bile, serum, plasma,urine, synovial fluid or spinal fluid) or another tissue or cell sampletaken from an individual having such a disorder, relative to thestandard gene expression level, i.e., the expression level in healthytissue or bodily fluid from an individual not having the disorder.

Preferred epitopes include those comprising a sequence shown in SEQ IDNO:50 as residues: Ser-3 to Pro-9, Leu-17 to Leu-29, Asp-64 to Pro-69,Ile-105 to Gln-110, Thr-183 to Gln-200, Cys-239 to Arg-247, Ser-256 toMet-261, Gln-280 to Ala-296, Arg-310 to Thr-321, Lys-363 to Asp-368,Ser-395 to Trp-400, Thr-443 to Asp-453.

The tissue distribution in a variety of immune cells and tissuesindicates that polynucleotides and polypeptides corresponding to thisgene are useful for replacement therapy in a variety of immune systemdisorders. Furthermore, polynucleotides and polypeptides correspondingto this gene are useful for the diagnosis and/or treatment ofhematopoietic disorders. This gene product is primarily expressed inhematopoietic cells and tissues, suggesting that it plays a role in thesurvival, proliferation, and/or differentiation of hematopoieiticlineages. This is particularly supported by the expression of this geneproduct in liver, which is a primary site of definitive hematopoiesisduring development. Expression of this gene product in T cells andprimary dendritic cells also strongly indicates a role for this proteinin immune function and immune surveillance. Protein, as well as,antibodies directed against the protein may show utility as a tumormarker and/or immunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:14 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 2257 of SEQID NO:14, b is an integer of 15 to 2271, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:14, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 5

The gene encoding the disclosed cDNA is thought to reside on chromosome15. Accordingly, polynucleotides related to this invention are useful asa marker in linkage analysis for chromosome 15.

This gene is expressed primarily in brain.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, neural disorders,particularly neurodegenerative and behaviour conditions, such as mooddisorders, schizophrenia and related diseases, bipolar disorder andunipolar depression. Similarly, polypeptides and antibodies directed tothese polypeptides are useful in providing immunological probes fordifferential identification of the tissue(s) or cell type(s). For anumber of disorders of the above tissues or cells, particularly of thecentral nervous system, expression of this gene at significantly higheror lower levels may be routinely detected in certain tissues or celltypes (e.g. brain, and cancerous and wounded tissues) or bodily fluids(e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid) oranother tissue or cell sample taken from an individual having such adisorder, relative to the standard gene expression level, i.e., theexpression level in healthy tissue or bodily fluid from an individualnot having the disorder.

Preferred epitopes include those comprising a sequence shown in SEQ IDNO:51 as residues: Met-1 to Gly-8, Pro-10 to Arg-17, Pro-45 to Ser-55,Gly-63 to Tyr-74.

The tissue distribution in brain indicates that polynucleotides andpolypeptides corresponding to this gene are useful for thedetection/treatment of neurodegenerative disease states and behaviouraldisorders such as Alzheimers Disease, Parkinsons Disease, HuntingtonsDisease, schizophrenia, mania, dementia, paranoia, obsessive compulsivedisorder and panic disorder. Also given the brain-specific expression ofthis gene, the promoter region of this gene may contain a brain-specificelement that could be used for targeting expression of vector systems tothe brain in gene replacement therapy. Protein, as well as, antibodiesdirected against the protein may show utility as a tumor marker and/orimmunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:15 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 612 of SEQID NO:15, b is an integer of 15 to 626, where both a and b correspond tothe positions of nucleotide residues shown in SEQ ID NO:15, and where bis greater than or equal to a+14.

Features of Protein Encoded by Gene No: 6

This gene maps to chromosome 1 and therefore, polynucleotides of theinvention can be used in linkage analysis as a marker for chromosome 1.

This gene is expressed abundantly in rhabdomyosarcoma, and is expressedto a high level in different regions of the brain and pituitary gland.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, neurological,muscular, or endocrine disorders, particularly soft tissue tumors, suchas fibroids. Similarly, polypeptides and antibodies directed to thesepolypeptides are useful in providing immunological probes fordifferential identification of the tissue(s) or cell type(s). For anumber of disorders of the above tissues or cells, particularly of thebrain, expression of this gene at significantly higher or lower levelsmay be routinely detected in certain tissues or cell types (e.g. brain,muscle, endocrine, and cancerous and wounded tissues) or bodily fluids(e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid) oranother tissue or cell sample taken from an individual having such adisorder, relative to the standard gene expression level, i.e., theexpression level in healthy tissue or bodily fluid from an individualnot having the disorder.

The tissue distribution in rhadomyosarcoma tissue indicates a role forthe protein product either in the detection and/or treatment ofmusculo-skeletal disorders including muscle degeneration, musclewasting, rhabdomyolysis, muscular dystrophy, cardiomyopathy, fibroids,myomas, and rhabdomyosarcomas. Furthermore, expression in the brainindicates a role for the protein product of this gene in thedetection/treatment of neurodegenerative disease states and behaviouraldisorders such as Alzheimers Disease, Parkinsons Disease, HuntingtonsDisease, schizophrenia, mania, dementia, paranoia, obsessive compulsivedisorder and panic disorder. Protein, as well as, antibodies directedagainst the protein may show utility as a tumor marker and/orimmunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:16 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 2104 of SEQID NO:16, b is an integer of 15 to 2118, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:16, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 7

The translation product of this gene shares sequence homology with theTDAG51 gene which is thought to be important in the mediation ofapoptosis and cell death by coupling TCR stimulation to Fas expression.In specific embodiments, the polypeptides of the invention comprise thesequence: KELSFARIKAVECVESTGRHIYFTLV (SEQ ID NO:110) and/or GWNAQITLGLVKFKNQQ (SEQ ID NO:111). The gene encoding the disclosed cDNA is thoughtto reside on chromosome 1. Accordingly, polynucleotides related to thisinvention are useful as a marker in linkage analysis for chromosome 1.

This gene is expressed in breast cancer tissue, and to a lesser extent,in macrophage.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, immune or reproductivedisorders, particularly breast cancer. Similarly, polypeptides andantibodies directed to these polypeptides are useful in providingimmunological probes for differential identification of the tissue(s) orcell type(s). For a number of disorders of the above tissues or cells,particularly of the immune system, expression of this gene atsignificantly higher or lower levels may be routinely detected incertain tissues or cell types (e.g. breast, immune, and cancerous andwounded tissues) or bodily fluids (e.g., lymph, breast milk, serum,plasma, urine, synovial fluid or spinal fluid) or another tissue or cellsample taken from an individual having such a disorder, relative to thestandard gene expression level, i.e., the expression level in healthytissue or bodily fluid from an individual not having the disorder.

Preferred epitopes include those comprising a sequence shown in SEQ IDNO:54 as residues: Met-1 to Pro-9, Gln-43 to Glu-49, Phe-95 to Arg-102.

The tissue distribution in breast cancer tissue, combined with thehomology to the TDAG51 gene indicates that polynucleotides andpolypeptides corresponding to this gene are useful for diagnosis andintervention of immune disorders, such as immunodeficiency, allergy,infection, inflammation, and tissue/organ transplantation.Alternatively, the tissue distribution in tumors of breast originsindicates that polynucleotides and polypeptides corresponding to thisgene are useful for the diagnosis and intervention of these tumors,particularly during antigen presentation early in the immune response.Protein, as well as, antibodies directed against the protein may showutility as a tissue-specific marker and/or immunotherapy target for theabove listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:17 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 1062 of SEQID NO:17, b is an integer of 15 to 1076, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:17, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 8

The gene encoding the disclosed cDNA is thought to reside onchromosome 1. Accordingly, polynucleotides related to this invention areuseful as a marker in linkage analysis for chromosome 1. One embodimentof this gene comprises the polypeptides of the following amino acidsequence:MVTTIVLGRRFIGSIVKEASQRGKVSLFRSILLFLTRFTVLTATGWSLCRSLIHLFRTYSFLNLLFLCYPFGMYIPFLQLNXXLRKTSLFNHMASMGPREAVSGLAKSRDYLLTLRETWKQHXRQLYGPDAMPTHACCLSPSLIRSEVEFLKMDFNWRMKEVLVSSMLSAYYVAFVPVWFVKNTHYYDKRWSCXTLPAGVHQHLRDPHAAPAACQLL (SEQ ID NO:112), MVTTIVLGRRFIGSIVKEASQRGKVS (SEQ ID NO:113),LFRSILLFLTRFTVLTATGWSLC (SEQ ID NO:114), RSLIHLFRTYSFLNLLFLCYPFGMYIPFLQ(SEQ ID NO:115), LNXXLRKTSLFNHMASMGPREAVSGLAKSR (SEQ ID NO:116),DYLLTLRETWKQHXRQLYGPDAMPTHACCL (SEQ ID NO:117),SPSLIRSEVEFLKMDFNWRMKEVLVSSMLSA (SEQ ID NO:118),YYVAFVPVWFVKNTHYYDKRWSCXTLP (SEQ ID NO:119), and/or AGVHQHLRDPHAAPAACQLL(SEQ ID NO:120). An additional embodiment is the polynucleotidesencoding these polypeptides.

This gene is expressed in breast tissue, amniotic cells, and to a lesserextent, in smooth muscle, T-cells, and infant brain.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, reproductive ordevelopmental disorders, particularly fetal distress syndrome andembryonic wasting. Similarly, polypeptides and antibodies directed tothese polypeptides are useful in providing immunological probes fordifferential identification of the tissue(s) or cell type(s). For anumber of disorders of the above tissues or cells, particularly of thefemale reproductive system, expression of this gene at significantlyhigher or lower levels may be routinely detected in certain tissues orcell types (e.g. breast, fetal, neural, immune, hematopoietic, muscular,and cancerous and wounded tissues) or bodily fluids (e.g., lymph,amniotic fluid, serum, plasma, urine, synovial fluid or spinal fluid) oranother tissue or cell sample taken from an individual having such adisorder, relative to the standard gene expression level, i.e., theexpression level in healthy tissue or bodily fluid from an individualnot having the disorder.

The tissue distribution in breast tissue indicates that polynucleotidesand polypeptides corresponding to this gene are useful for the diagnosisand/or treatment of reproductive disorders. Alternately, this geneproduct may be produced by the placenta and then transported to theembryo, where it may play a crucial role in the development and/orsurvival of the developing embryo or fetus. Expression of this geneproduct in a vascular-rich tissue such as the breast and amnion alsoindicates that this gene product may be produced more generally inendothelial cells or within the circulation. In such instances, it mayplay more generalized roles in vascular function, such as inangiogenesis. It may also be produced in the vasculature and haveeffects on other cells within the circulation, such as hematopoieticcells. It may serve to promote the proliferation, survival, activation,and/or differentiation of hematopoietic cells, as well as other cellsthroughout the body. Protein, as well as, antibodies directed againstthe protein may show utility as a tumor marker and/or immunotherapytargets for the above listed tissues.

Features of Protein Encoded by Gene No: 9

In specific embodiments, the polypeptides of the invention comprise thesequence: LVLGLSXLNNSYNFSF (SEQ ID NO:121), HVVIGSQAEEGQYSLNF (SEQ IDNO:122), HNCNNSVPGKEHPFDITVM (SEQ ID NO:123), FIKYVLSDKEKKVFGIV (SEQ IDNO:124), IPMQVLANVAYII (SEQ ID NO:125), IPMQVLANVAYII (SEQ ID NO:126),DGKVAVNLAKLKLFR (SEQ ID NO:127), and/or IREKNPDGFLSAA (SEQ ID NO:128).Polynucleotides encoding these polypepides are also encompassed by theinvention. The gene encoding the disclosed cDNA is thought to reside onchromosome 19. Accordingly, polynucleotides related to this inventionare useful as a marker in linkage analysis for chromosome 19.

This gene is primarily expressed in the fetal liver/spleen and pituitarygland.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, immune, hematopoietic,or endocrine disorders, particularly cancers and other proliferatveconditions. Similarly, polypeptides and antibodies directed to thesepolypeptides are useful in providing immunological probes fordifferential identification of the tissue(s) or cell type(s). For anumber of disorders of the above tissues or cells, particularly of thehepatic, immune and hematopoetic systems, expression of this gene atsignificantly higher or lower levels may be routinely detected incertain tissues or cell types (e.g. liver, spleen, pituitary,developmental, and cancerous and wounded tissues) or bodily fluids(e.g., lymph, amniotic fluid, serum, plasma, urine, synovial fluid orspinal fluid) or another tissue or cell sample taken from an individualhaving such a disorder, relative to the standard gene expression level,i.e., the expression level in healthy tissue or bodily fluid from anindividual not having the disorder.

Preferred epitopes include those comprising a sequence shown in SEQ IDNO:55 as residues: Ser-62 to Cys-71, Thr-78 to Leu-86, Ser-104 toLys-109, Ser-130 to Ala-135, Gln-168 to Asp-174.

The tissue distribution in fetal liver/spleen indicates thatpolynucleotides and polypeptides corresponding to this gene are usefulfor the diagnosis and treatment of hepatic disorders, and disorders ofthe immune and hematopoetic systems, such as hepatic failure, hepatitis,alcoholic liver diseases, portal hypertension, toxic liver injury, livertransplantation, and neoplasm of the liver. The expression in the fetalliver spleen also indicate its function in hematopiesis, and thereforethe gene may be useful in hematopoietic disorders including anemia,leukemia or cancer radiotherapy/chemotherapy. The expression in thepituitary gland may indicate its use in endocrine disorders withsystemic or specific manifestations. Protein, as well as, antibodiesdirected against the protein may show utility as a tumor marker and/orimmunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:19 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 1323 of SEQID NO:19, b is an integer of 15 to 1337, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:19, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 10

The translation product of this gene shares sequence homology with a DNAbinding protein from Gallus gallus which is thought to be important intranscriptional regulation of gene expression. In specific embodiments,polypeptides of the invention comprise the sequence: MMFGGYETI (SEQ IDNO:129), YRDESSSELSVDSEVEFQLYSQIH (SEQ ID NO:130),YAQDLDDVIREEEHEEKNSGNSESSSSKPNQKKLIVLSDSEVIQLSDGSEVITLSDEDSIYRCKGKNVRVQAQENAHGLSSSLQSNELVDKKCKSDIEKPKSEERSGVIREVMIIEVSSSEEEESTISEGDNVESW (SEQ IDNO:131), MLLGCEVDDIKDDDILLNLVGCENSVTEGEDGINWSIS (SEQ ID NO:132),DKDIEAQIANNRTPGRWT (SEQ ID NO:133), QRYYSANKNIICRNCDKRGHLSKNCPLPRKV (SEQID NO:134), and/orRRCFLCSRRGHLLYSCPAPLCEYCPVPKMLDHSCLFRHSWDKQCDRCHMLGHYTDACTEIWRQYHLTTKPGPPKKPKTPSRPSALAYCYHCAQKGHYGHECPEREVYDPSPVSPFICYYXDKYEIQEREKRLKQKIKVXKKNGVIPEPSKLPYIKAANENPHHDIRKGRASWKSNRWPQ (SEQ ID NO:135). Polynucleotidesencoding these polypeptides are also encompassed by the invention.

This gene is expressed in tonsils and bone marrow.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, disorders of theimmune, hematopoetic, and lymphatic systems. Similarly, polypeptides andantibodies directed to these polypeptides are useful in providingimmunological probes for differential identification of the tissue(s) orcell type(s). For a number of disorders of the above tissues or cells,particularly of the immune, hematopoetic, and lymph systems, expressionof this gene at significantly higher or lower levels may be routinelydetected in certain tissues or cell types (e.g. immune, hematopoietic,and cancerous and wounded tissues) or bodily fluids (e.g., lymph, serum,plasma, urine, synovial fluid or spinal fluid) or another tissue or cellsample taken from an individual having such a disorder, relative to thestandard gene expression level, i.e., the expression level in healthytissue or bodily fluid from an individual not having the disorder.

The tissue distribution in bone marrow and tonsil tissues, combined withthe homology to a DNA binding protein indicates that polynucleotides andpolypeptides corresponding to this gene are useful for the treatment anddiagnosis of disorders in the immune, hematopoetic, and lymph systems.Furthermore, expression of this gene product in tonsils indicates a rolein the regulation of the proliferation; survival; differentiation;and/or activation of potentially all hematopoietic cell lineages,including blood stem cells. This gene product may be involved in theregulation of cytokine production, antigen presentation, or otherprocesses that may also suggest a usefulness in the treatment of cancer(e.g. by boosting immune responses). Since the gene is expressed incells of lymphoid origin, the gene or protein, as well as, antibodiesdirected against the protein may show utility as a tumor marker and/orimmunotherapy targets for the above listed tissues. Therefore it may bealso used as an agent for immunological disorders including arthritis,asthma, immune deficiency diseases such as AIDS, leukemia, rheumatoidarthritis, inflammatory bowel disease, sepsis, acne, and psoriasis. Inaddition, this gene product may have commercial utility in the expansionof stem cells and committed progenitors of various blood lineages, andin the differentiation and/or proliferation of various cell types.Protein, as well as, antibodies directed against the protein may showutility as a tumor marker and/or immunotherapy targets for the abovelisted tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:20 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 1376 of SEQID NO:20, b is an integer of 15 to 1390, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:20, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 11

One embodiment of this gene comprises polypeptides of the followingamino acid sequence: (SEQ ID NO:136)MSFPPHLNRPPMGIPALPPGIPPPQFPGFPPPVPPGTPMIPVPMSIMAPAPTVLVPTVSMVGKHLGARKDHPGLKAKENDENCGPTTTVFVGNISEKASDMLIRQLLAKCGLVLSWKRVQGASGKLQAFGFCEYKEPESTLRALRLLHDLQIGEKKLLVKVDAKTKAQLDEWKAKKKASNGNARPETVTNDDEEALDEETKRRDQMIKGAIEVLIREYSSELNAPSQESDSHPRKKKKEKKEDIFRRFPVAPLIPYPLITKEDINAIEMEEDKRDLISREISKFRDTHKKLEEEKGKKEKERQEIEKERRERERERERERERREREREREREREREKEKERERERERDRDRDRTKERDRDRDRERDRDRDRERSSDRNKDRIRSREKSRDRERERERERE REREPERERERERERE,(SEQ ID NO:137) MSFPPHLNRPPMGIPALPPGIPPPQFPGFPPPVPPGTPMIPVP, (SEQ IDNO:138) MSIMAPAPTVLVPTVSMVGKHLGARKDHPGLKAKE, (SEQ ID NO:139)NDENCGPTTTVFVGNISEKASDMLIRQLLAKCGLVLSWKRV, (SEQ ID NO:140)QGASGKLQAFGFCEYKEPESTLRALRLLHDLQIGEKKLLV, (SEQ ID NO:141)KVDAKTKAQLDEWKAKKKASNGNARPETVTNDDEEALDE, (SEQ ID NO:142)ETKRRDQMIKGAIEVLIREYSSELNAPSQESDSHPRKKKK, (SEQ ID NO:143)EKKEDIFRRFPVAPLIPYPLITKEDINAIEMEEDKRDLISREIS, (SEQ ID NO:144)KFRDTHKKLEEEKGKKEKERQEIEKERRERERERERERERR, (SEQ ID NO:145)EREREREREREREKEKERERERERDRDRDRTKERDRDRDREK, and/or (SEQ ID NO:146)RDRDRDRERSSDRNKDRIRSREKSRDRERERERERERERERERERERERE RE.Polynucleotides encoding these polypeptides are also encompassed by theinvention.

This gene is expressed in fetal liver/spleen, dendritic, and T-cells.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, immune orhematopoietic disorders. Similarly, polypeptides and antibodies directedto these polypeptides are useful in providing immunological probes fordifferential identification of the tissue(s) or cell type(s). For anumber of disorders of the above tissues or cells, particularly of theimmune system, expression of this gene at significantly higher or lowerlevels may be routinely detected in certain tissues or cell types (e.g.immune, hematopoietic, and cancerous and wounded tissues) or bodilyfluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinalfluid) or another tissue or cell sample taken from an individual havingsuch a disorder, relative to the standard gene expression level, i.e.,the expression level in healthy tissue or bodily fluid from anindividual not having the disorder.

The tissue distribution in immune cells and tissues indicates that theprotein products of this gene are useful for the treatment and diagnosisof immune system disorders, particularly those involving dendritic orT-cells such as inflammation. Furthermore, this gene product isprimarily expressed in hematopoietic cells and tissues, suggesting thatit plays a role in the survival, proliferation, and/or differentiationof hematopoieitic lineages. This is particularly supported by theexpression of this gene product in fetal liver, which is a primary siteof definitive hematopoiesis. Expression of this gene product in T cellsand primary dendritic cells also strongly indicates a role for thisprotein in immune function and immune surveillance. Protein, as well as,antibodies directed against the protein may show utility as a tumormarker and/or immunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:21 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 1417 of SEQID NO:21, b is an integer of 15 to 1431, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:21, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 12

Preferred polypeptides encoded by this gene include the following:MGLNPPGLTSALKPQMEGRLVGGGGSFSSRGRHPAGWVLPQPCLLLSPTLSFPPACGLLVPSPSLLPAVSSYHLPLGRGLIRPAFKIKVCSKLTVWCSLPSPSRWRCCHGNAVALPALGPWRXWEQGSAVRSPAFPVRQAWLPCSGSLTSW (SEQ ID NO:150), KPQMEGRLVGGGGSFSSRGRHP (SEQ ID NO:147),LLVPSPSLLPAVSSYHLPLGRGLIR (SEQ ID NO:148), and/orEQGSAVRSPAFPVRQAWLPCSGS (SEQ ID NO:149). Also provided arepolynucleotides encoding such polypeptides.

This gene is expressed in activated neutrophils, endothelial cells, Tcells, and to a lesser extent, in brain and liver.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, immune, hematopoietic,integumentary, or vascular disorders, particularly immunodeficienciessuch as AIDS, and susceptiblity to infectious disease. Similarly,polypeptides and antibodies directed to these polypeptides are useful inproviding immunological probes for differential identification of thetissue(s) or cell type(s). For a number of disorders of the abovetissues or cells, particularly of the immune system and skin, expressionof this gene at significantly higher or lower levels may be routinelydetected in certain tissues or cell types (e.g. brain, immune,integumentary, and cancerous and wounded tissues) or bodily fluids(e.g., lymph, serum, plasma, urine, synovial fluid or spinal fluid) oranother tissue or cell sample taken from an individual having such adisorder, relative to the standard gene expression level, i.e., theexpression level in healthy tissue or bodily fluid from an individualnot having the disorder.

Preferred epitopes include those comprising a sequence shown in SEQ IDNO:58 as residues: Glu-41 to Val-46.

The tissue distribution in immune cells indicates that the gene productis useful for the diagnosis and/or treatment of a variety of disorders,including hematopoietic disorders, neurological disorders, liverdisease, and disorders involving angiogenesis. The expression of thisgene product in hematopoietic cells and tissues indicates that it playsa role in the survival, proliferation, and/or differentiation ofhematopoieitic lineages. This is particularly supported by theexpression of this gene product in fetal liver, which is a primary siteof definitive hematopoiesis. Expression of this gene product in T cellsand neutrophils also strongly indicates a role for this protein inimmune function and immune surveillance. Additionally, the tissuedistribution indicates that polynucleotides and polypeptidescorresponding to this gene are useful for the detection/treatment ofneurodegenerative disease states and behavioural disorders such asAlzheimers Disease, Parkinsons Disease, Huntingtons Disease, TouretteSyndrome, schizophrenia, mania, dementia, paranoia, obsessive compulsivedisorder, panic disorder, learning disabilities, ALS, psychoses, autism,and altered bahaviors, including disorders in feeding, sleep patterns,balance, and perception. In addition, the gene or gene product may alsoplay a role in the treatment and/or detection of developmental disordersassociated with the developing embryo, or sexually-linked disorders.Moreover, expression within endothelial cells indicates that the proteinis useful in the treatment and/or diagnosis of a variety of vasculardisorders, which include, but are not limited to, embolism, aneurysm,microvascular disease, atherosclerosis, and stroke. Protein, as well as,antibodies directed against the protein may show utility as a tumormarker and/or immunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:22 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 2525 of SEQID NO:22, b is an integer of 15 to 2539, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:22, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 13

This gene is expressed in keratinocytes, and to a lesser extent, inendothelial cells and placenta.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, integumentary orvascular disorders, particularly impaired wound healing and autoimmunedisorders. Similarly, polypeptides and antibodies directed to thesepolypeptides are useful in providing immunological probes fordifferential identification of the tissue(s) or cell type(s). For anumber of disorders of the above tissues or cells, particularly of theskin, expression of this gene at significantly higher or lower levelsmay be routinely detected in certain tissues or cell types (e.g.integumentary, endothelial, and cancerous and wounded tissues) or bodilyfluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinalfluid) or another tissue or cell sample taken from an individual havingsuch a disorder, relative to the standard gene expression level, i.e.,the expression level in healthy tissue or bodily fluid from anindividual not having the disorder.

Preferred epitopes include those comprising a sequence shown in SEQ IDNO:59 as residues: Pro-35 to Trp-42, Ala-53 to Asp-62, Arg-103 toPro-113.

The tissue distribution in keratinocytes indicates that the proteinproducts of this gene are useful for the treatment of wound healingdeficiency and skin disorders, including congenital disorders (i.e.nevi, moles, freckles, Mongolian spots, hemangiomas, port-winesyndrome), integumentary tumors (i.e. keratoses, Bowen's disease, basalcell carcinoma, squamous cell carcinoma, malignant melanoma, Paget'sdisease, mycosis fungoides, and Kaposi's sarcoma), injuries andinflammation of the skin (i.e. wounds, rashes, prickly heat disorder,psoriasis, dermatitis), atherosclerosis, uticaria, eczema,photosensitivity, autoimmune disorders (i.e. lupus erythematosus,vitiligo, dermatomyositis, morphea, scleroderma, pemphigoid, andpemphigus), keloids, striae, erythema, petechiae, purpura, andxanthelasma. Moreover, such disorders may predispose increasedsusceptibility to viral and bacterial infections of the skin (i.e. coldsores, warts, chickenpox, molluscum contagiosum, herpes zoster, boils,cellulitis, erysipelas, impetigo, tinea, althletes foot, and ringworm).Moreover, expression within endothelial cells and pancreatic tissuesindicates that the protein product of this gene may be useful in thetreatment and/or prevention of a variety of vascular disorders,particularly those involving highly vascularized tissues, which include,but are not limited to, embolism, aneurysm, stroke, atherosclerosis, andmiscrovascular disease. Protein, as well as, antibodies directed againstthe protein may show utility as a tumor marker and/or immunotherapytargets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:23 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 1027 of SEQID NO:23, b is an integer of 15 to 1041, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:23, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 14

Preferred polypeptides encoded by this gene comprise the following aminoacid sequence:NVTKITLESFLAWKKRKRQEKIDKLEQDMERRKADFKAGKALVISGREVFEFRPELVNDDDEEA (SEQ IDNO:151), and/or ERRKADFKAGKALVISGREVFE (SEQ ID NO:152). Polynucleotidesencoding these polypeptides are also encompassed by the invention. Thegene encoding the disclosed cDNA is thought to reside on chromosome 2.Accordingly, polynucleotides related to this invention are useful as amarker in linkage analysis for chromosome 2.

This gene is expressed in kidney, and to a lesser extent, in embryonictissues.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, renal, urogenital, ordevelopmental disorders, particularly renal failure. Similarly,polypeptides and antibodies directed to these polypeptides are useful inproviding immunological probes for differential identification of thetissue(s) or cell type(s). For a number of disorders of the abovetissues or cells, particularly of the kidney, expression of this gene atsignificantly higher or lower levels may be routinely detected incertain tissues or cell types (e.g. kidney, developmental, and cancerousand wounded tissues) or bodily fluids (e.g., lymph, amniotic fluid,serum, plasma, urine, synovial fluid or spinal fluid) or another tissueor cell sample taken from an individual having such a disorder, relativeto the standard gene expression level, i.e., the expression level inhealthy tissue or bodily fluid from an individual not having thedisorder.

The tissue distribution in kidney indicates that this gene or geneproduct could be used in the treatment and/or detection of kidneydiseases including renal failure, nephritus, renal tubular acidosis,proteinuria, pyuria, edema, pyelonephritis, hydronephritis, nephroticsyndrome, crush syndrome, glomerulonephritis, hematuria, renal colic andkidney stones, in addition to Wilms Tumor Disease, and congenital kidneyabnormalities such as horseshoe kidney, polycystic kidney, and Falconi'ssyndrome. Expression within embryonic tissue indicates that this proteinmay play a role in the regulation of cellular division, and may showutility in the diagnosis and treatment of cancer and other proliferativedisorders. Similarly, developmental tissues rely on decisions involvingcell differentiation and/or apoptosis in pattern formation. Thus thisprotein may also be involved in apoptosis or tissue differentiation andcould again be useful in cancer therapy. Protein, as well as, antibodiesdirected against the protein may show utility as a tumor marker and/orimmunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:24 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 1948 of SEQID NO:24, b is an integer of 15 to 1962, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:24, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 15

The gene encoding the disclosed cDNA is thought to reside on chromosome22. Accordingly, polynucleotides related to this invention are useful asa marker in linkage analysis for chromosome 22.

This gene is expressed primarily in brain, and to a lesser extent, inliver.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, neural or hepaticdisorders, particularly depression, manic depression and otherneurodegenerative diseases. Similarly, polypeptides and antibodiesdirected to these polypeptides are useful in providing immunologicalprobes for differential identification of the tissue(s) or cell type(s).For a number of disorders of the above tissues or cells, particularly ofthe central nervous system, expression of this gene at significantlyhigher or lower levels may be routinely detected in certain tissues orcell types (e.g. brain, liver, cancerous and wounded tissues) or bodilyfluids (e.g., lymph, bile, serum, plasma, urine, synovial fluid orspinal fluid) or another tissue or cell sample taken from an individualhaving such a disorder, relative to the standard gene expression level,i.e., the expression level in healthy tissue or bodily fluid from anindividual not having the disorder.

The tissue distribution in brain indicates that the protein products ofthis gene are useful for the treatment of central nervous systemdisorders such as depression and other mental illnesses, andneurodegenerative disorders, such as Alzheimers Disease, ParkinsonsDisease, Huntingtons Disease, Tourette Syndrome, schizophrenia, mania,dementia, paranoia, obsessive compulsive disorder, panic disorder,learning disabilities, ALS, psychoses, autism, and altered bahaviors,including disorders in feeding, sleep patterns, balance, and perception.In addition, the gene or gene product may also play a role in thetreatment and/or detection of developmental disorders associated withthe developing embryo, or sexually-linked disorders. Moreover, theexpression within liver tissue indicates that polynucleotides andpolypeptides corresponding to this gene are useful for the detection andtreatment of liver disorders and cancers (e.g. hepatoblastoma, jaundice,hepatitis, liver metabolic diseases and conditions that are attributableto the differentiation of hepatocyte progenitor cells). Protein, as wellas, antibodies directed against the protein may show utility as a tumormarker and/or immunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:25 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 1214 of SEQID NO:25, b is an integer of 15 to 1228, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:25, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 16

The translation product of this gene shares homology with Prefoldin,which is believed to function as a chaperone that delivers unfoldedproteins to cytosolic chaperonins (Cell 93, 863-873 (1998)). In specificembodiments, polypeptides of the invention comprise the following aminoacid sequence:MCDELPGEGRWEPGQDRKLCLSFPLGTPARPIKSVCPTLLSLVFLSRGMEQRVREAVAVSTSAPAPSASEPFLSWGMGLAXFSFPFLYL (SEQ ID NO:153),GASLGSSSSCPSHSWWGQRSVCRETASPLPRWMLYLDGLATSHFLHHPEPHLLPSPGVFTRLCCHLCPGHXSLSGCVMNSQEREDGSQGKIGSSA (SEQ ID NO:154),TSVLSSSSVYCMQARKLSVSQRYRKGKEKXARPIPQERKGSDAEGAGAEVETATASLTLCSIPLLKKTRLSRVGQTLFIGLAGVPSGKLRQSFLSCPGSHLPSPGSSSHIPRGKXVLGRGGSKAG (SEQ ID NO:155),ALVKGTGREKRRXQGPSPKKGRALMQREQELRWRRPLmPLSPSVPSLCSRKPGLAEWDRRFLLVWLACLVESSGRASYLALAPIFPLLGVHHTSREGXVSWAEVAAKPGKNSRAGKQMGLRVMQKM (SEQ IDNO:156), SFPLGTPARPIKSVCPTLLSLVFLSRGMEQRV (SEQ ID NO:157),TASPLPRWMLYLDGLATSHFLHHPEPHLLPS (SEQ ID NO:158),RKGSDAEGAGAEVETATASLTLCSIPLLKKT (SEQ ID NO:159),QREQELRWRRPLPLSPSVPSLCSRK (SEQ ID NO:160), and/orPLLGVHHTSREGXVSWAEVAAKPGKNSRA (SEQ ID NO:161). Polynucleotides encodingthese polypeptides are also encompassed by the invention. The geneencoding the disclosed cDNA is thought to reside on chromosome 5.Accordingly, polynucleotides related to this invention are useful as amarker in linkage analysis for chromosome 5.

This gene is expressed in fetal brain, and to a lesser extent, inplacenta, endothelial cells, fetal lung, and T cells.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, neural ordevelopmental disorders, particularly restinosis, birth defects andimmune disorders. Similarly, polypeptides and antibodies directed tothese polypeptides are useful in providing immunological probes fordifferential identification of the tissue(s) or cell type(s). For anumber of disorders of the above tissues or cells, particularly of thecardiovascular system, and developmental process, expression of thisgene at significantly higher or lower levels may be routinely detectedin certain tissues or cell types (e.g. brain, endothelial cells,developmental, immune, pulmonary, and cancerous and wounded tissues) orbodily fluids (e.g., lymph, pulmonary surfactant or sputum, serum,plasma, urine, synovial fluid or spinal fluid) or another tissue or cellsample taken from an individual having such a disorder, relative to thestandard gene expression level, i.e., the expression level in healthytissue or bodily fluid from an individual not having the disorder.

Preferred epitopes include those comprising a sequence shown in SEQ IDNO:62 as residues: Gln-36 to Lys-42, Glu-89 to Arg-104.

The tissue distribution in brain, combined with the homology toprefoldin indicates that the protein products of this gene are usefulfor the development of agonists and/or antagonists for for treatment ofnervous system disorders and fetal developmental disorder, andsindicates that the translation product of this gene is useful in thedetection and/or treatment of diseases associated with the improperdelivery of unfolded proteins to cytosolic chaperonins. Furthermore, thetissue distribution indicates that polynucleotides and polypeptidescorresponding to this gene are useful for the detection/treatment ofneurodegenerative disease states and behavioural disorders such asAlzheimers Disease, Parkinsons Disease, Huntingtons Disease, TouretteSyndrome, schizophrenia, mania, dementia, paranoia, obsessive compulsivedisorder, panic disorder, learning disabilities, ALS, psychoses, autism,and altered bahaviors, including disorders in feeding, sleep patterns,balance, and perception. In addition, the gene or gene product may alsoplay a role in the treatment and/or detection of developmental disordersassociated with the developing embryo, sexually-linked disorders, ordisorders of the cardiovascular system. Protein, as well as, antibodiesdirected against the protein may show utility as a tumor marker and/orimmunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:26 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 1326 of SEQID NO:26, b is an integer of 15 to 1340, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:26, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 17

In specific embodiments, polypeptides of the invention comprise thefollowing amino acid sequence:MSVLKGERQQTLALAVLSVAKENARDVCCLQGWQDTSCRDTSCAALRGGLQTLFPAPVHFRCGGPAELKGRGS (SEQ ID NO:162),AHSFTTPEEARGAGSMGCRFPFKHTHSPHPRRPEVQGAWAGCTSAGEKAEPPPSREPGSQASRFPLPP(SEQ ID NO:163), GWQDTSCRDTSCAALRGGLQTLFPA (SEQ ID NO:164), and/orGCRFPFKHTHSPHPRRPEVQGAWA (SEQ ID NO:165). Polynucleotides encoding thesepolypeptides are also encompassed by the invention.

This gene is expressed in hemangiopericytoma, and to a lesser extent, infetal tissues.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, developmentaldisorders, particularly hemangiopericytomas and other soft-tissuecancers, as well as other proliferative disorders. Similarly,polypeptides and antibodies directed to these polypeptides are useful inproviding immunological probes for differential identification of thetissue(s) or cell type(s). For a number of disorders of the abovetissues or cells, expression of this gene at significantly higher orlower levels may be routinely detected in certain tissues or cell types(e.g. fetal, kidney, and cancerous and wounded tissues) or bodily fluids(e.g., lymph, amniotic fluid, serum, plasma, urine, synovial fluid orspinal fluid) or another tissue or cell sample taken from an individualhaving such a disorder, relative to the standard gene expression level,i.e., the expression level in healthy tissue or bodily fluid from anindividual not having the disorder.

Preferred epitopes include those comprising a sequence shown in SEQ IDNO:63 as residues: Glu-43 to Pro-51, Gly-71 to Arg-82, Pro-96 toArg-103, Thr-130 to Gly-140.

The polynucleotides and polypeptides related to this gene are believedto be useful for the treatment and diagnosis of tumors, particularlyhemangiopericytomas, and for the treatment of developmental disorders.Furthermore, the tissue distribution indicates that polynucleotides andpolypeptides corresponding to this gene are useful for the diagnosisand/or treatment of disorders of the developing embryo, where it mayplay a crucial role in the development and/or survival of the developingembryo or fetus. Expression of this gene product in a vascular-richtissue such as the placenta also indicates that this gene product may beproduced more generally in endothelial cells or within the circulation.In such instances, it may play more generalized roles in vascularfunction, such as in angiogenesis. It may also be produced in thevasculature and have effects on other cells within the circulation, suchas hematopoietic cells. It may serve to promote the proliferation,survival, activation, and/or differentiation of hematopoietic cells, aswell as other cells throughout the body.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:27 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 792 of SEQID NO:27, b is an integer of 15 to 806, where both a and b correspond tothe positions of nucleotide residues shown in SEQ ID NO:27, and where bis greater than or equal to a+14.

Features of Protein Encoded by Gene No: 18

In specific embodiments, polypeptides of the invention comprise thefollowing amino acid sequence:PHQVEGRLGTMETWDSSHEGLLHCRIPLKGSWVQEPSCQYQWRRTRCMGIPPATSGWPCRAPAFLCARAEFPASPGGSTNF (SEQ ID NO:166),LVTPPSGGETGDHGNMGQLPRRALALQNSTQGILGPGAELPVSVEKDKVHGDPASNIRMAMPGTRFPLCSCRIPCQPGGIH (SEQ ID NO:167), EGLLHCRIPLKGSWVQEPSCQYQWRRTRCMGI (SEQ IDNO:168), and/or QNSTQGILGPGAELPVSVEKDKVHGDPAS (SEQ ID NO:169).Polynucleotides encoding these polypeptides are also encompassed by theinvention.

This gene is expressed in fetal liver, and to a lesser extent, in brainand T cells.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, neural, developmental,hepatic, or immune and hematopoietic disorders. Similarly, polypeptidesand antibodies directed to these polypeptides are useful in providingimmunological probes for differential identification of the tissue(s) orcell type(s). For a number of disorders of the above tissues or cells,particularly of the hepatic system, nervous system and immune system,expression of this gene at significantly higher or lower levels may beroutinely detected in certain tissues or cell types (e.g. immune, liver,brain, cancerous and wounded tissues) or bodily fluids (e.g., lymph,amniotic fluid, bile, serum, plasma, urine, synovial fluid or spinalfluid) or another tissue or cell sample taken from an individual havingsuch a disorder, relative to the standard gene expression level, i.e.,the expression level in healthy tissue or bodily fluid from anindividual not having the disorder.

The tissue distribution in brain indicates that the protein products ofthis gene are useful for the identification of agonists and/orantagonists for the treatment of mental illnesses such as schizophreniaand depression. The gene product may also be useful for monitoring fetaldevelopment during pregnancy. Furthermore, the expression of this geneproduct in fetal liver indicates a role in the regulation of theproliferation; survival; differentiation; and/or activation ofpotentially all hematopoietic cell lineages, including blood stem cells.This gene product may be involved in the regulation of cytokineproduction, antigen presentation, or other processes that may alsosuggest a usefulness in the treatment of cancer (e.g. by boosting immuneresponses). Since the gene is expressed in cells of lymphoid origin, thegene or protein, as well as, antibodies directed against the protein mayshow utility as a tumor marker and/or immunotherapy targets for theabove listed tissues. Therefore it may be also used as an agent forimmunological disorders including arthritis, asthma, immune deficiencydiseases such as AIDS, leukemia, rheumatoid arthritis, inflammatorybowel disease, sepsis, acne, and psoriasis. In addition, this geneproduct may have commercial utility in the expansion of stem cells andcommitted progenitors of various blood lineages, and in thedifferentiation and/or proliferation of various cell types.Alternatively, the tissue distribution indicates that polynucleotidesand polypeptides corresponding to this gene are useful for the detectionand treatment of liver disorders and cancers (e.g. hepatoblastoma,jaundice, hepatitis, liver metabolic diseases and conditions that areattributable to the differentiation of hepatocyte progenitor cells).Protein, as well as, antibodies directed against the protein may showutility as a tumor marker and/or immunotherapy targets for the abovelisted tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:28 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 682 of SEQID NO:28, b is an integer of 15 to 696, where both a and b correspond tothe positions of nucleotide residues shown in SEQ ID NO:28, and where bis greater than or equal to a+14.

Features of Protein Encoded by Gene No: 19

In specific embodiments, polypeptides of the invention comprise thefollowing amino acid sequence:FGTRKKYHLCMIPNLDLNLDRDLVLPDVSYQVESSEEDQSQT (SEQ ID NO:170),FLLSLGSLVMLLQDLVHSELDGTLHYTVALHKDGIEMSCEQSIDSPDFHLLDWKCTVEIHKEKKQQSLSLRIHSLRLILLTGFHLITXIWKHQISIQIEIQIGYHTQMVFFPRAE (SEQ ID NO:171),VHSELDGTLHYTVALHKDGIEMSCEQ (SEQ ID NO:172), and/orQSLSLRIHSLRLILLTGFHLITXIWKHQ (SEQ ID NO:173). Polynucleotides encodingthese polypeptides are also encompassed by the invention.

This gene is expressed in T cells, fetal liver, and to a lesser extentin brain.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, central nervousdiseases and immune or hematopoietic disorders. Similarly, polypeptidesand antibodies directed to these polypeptides are useful in providingimmunological probes for differential identification of the tissue(s) orcell type(s). For a number of disorders of the above tissues or cells,particularly of the central nervous system and immune system, expressionof this gene at significantly higher or lower levels may be routinelydetected in certain tissues or cell types (e.g. liver, immune, brain,cancerous and wounded tissues) or bodily fluids (e.g. lymph, serum,bile, amniotic fluid, plasma, urine, synovial fluid or spinal fluid) oranother tissue or cell sample taken from an individual having such adisorder, relative to the standard gene expression level, i.e., theexpression level in healthy tissue or bodily fluid from an individualnot having the disorder.

Preferred epitopes include those comprising a sequence shown in SEQ IDNO:65 as residues: Lys-69 to Leu-74, Ser-92 to Phe-97, Asp-109 toLeu-117, Leu-142 to Ser-159, Thr-166 to Glu-183, Ala-191 to Glu-205,Pro-213 to Glu-220.

The tissue distribution in T-cells and brain indicates that the proteinproducts of this gene are useful for the development of drugs for thetreatment of disorders affecting the central nervous system and immunesystem. The expression of this gene product primarily in hematopoieticcells and tissues indicates that it plays a role in the survival,proliferation, and/or differentiation of hematopoieitic lineages. Thisis particularly supported by the expression of this gene product infetal liver, which is a primary site of definitive hematopoiesis.Expression of this gene product in T cells also strongly indicates arole for this protein in immune function and immune surveillance.Protein, as well as, antibodies directed against the protein may showutility as a tumor marker and/or immunotherapy targets for the abovelisted tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:29 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 993 of SEQID NO:29, b is an integer of 15 to 1007, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:29, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 20

The translation product of this gene shares sequence homology with a C.elegans ORF that seems to be a transmembrane protein. (See Accession No.790406.) In specific embodiments, polypeptides of the invention comprisethe following amino acid sequence:MAAACGPGAAGTACSSACICFCDRGPCLGWNDPDRMLLRDVKALTLHYDRYTTSRSWIPSHSPQLKCVGGTAGCDSYTPKVIQCQNKGWDGYDVQWECKTDLDIAYKFGKTVVSCEGYESSEDQYVLRGSCGLEYNLDYTELGLQKLKESGKQHGFASFSDYYYKWSSADSCNMSGLITIVVLLGIAFVVYKLFLSDGQYSPPPYSEYPPFSHRYQRFTNSAGPPPPGFKSEFTGPQNTGHGATSGFGSAFTGQQGYENSGPGFWTGLGTGGILGYLFGSNRAATPFSDSWYYPSYPPSYPGTWNRAYSPLHGGSGSYSVCSNSDTKTRTASGYGGTRRR (SEQ IDNO:174), ACSSACICFCDRGPCLGWNDPDRM (SEQ ID NO:175),TAGCDSYTPKVIQCQNKGWDGYDVQW (SEQ ID NO:176),EYNLDYTELGLQKLKESGKQHGFASFSDYYYK (SEQ ID NO:177),YKLFLSDGQYSPPPYSEYPPFSHRYQRF (SEQ ID NO:178), ENSGPGFWTGLGTGGILGYLFGSNRA(SEQ ID NO:179), and/or NRAYSPLHGGSGSYSVCSNSDTKTR (SEQ ID NO:180).Polynucleotides encoding these polypeptides are also encompassed by theinvention. This gene maps to chromosome 8, and therefore can be used asa marker in linkage analysis for chromosome 8.

This gene is strongly expressed in fetal liver/spleen and pancreas, andto a lesser extent in T-cells, primary dendritic cells, bone marrowcells, and amygdala.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, reproductive, immune,hematopoietic, neural, or endocrine disorders, particularly cancer.Similarly, polypeptides and antibodies directed to these polypeptidesare useful in providing immunological probes for differentialidentification of the tissue(s) or cell type(s). For a number ofdisorders of the above tissues or cells, particularly of the immunesystem and endocrine system, expression of this gene at significantlyhigher or lower levels may be routinely detected in certain tissues orcell types (e.g. immune, pancreas, brain, cancerous and wounded tissues)or bodily fluids (e.g., lymph, serum, plasma, urine, synovial fluid orspinal fluid) or another tissue or cell sample taken from an individualhaving such a disorder, relative to the standard gene expression level,i.e., the expression level in healthy tissue or bodily fluid from anindividual not having the disorder.

Preferred epitopes include those comprising a sequence shown in SEQ IDNO:66 as residues: Gly-30 to Asp-35, Tyr-49 to Asp-59, Ala-71 to Thr-77,Gln-84 to Asp-92, Gln-94 to Thr-99, Glu-115 to Val-125, Lys-145 toLys-151, Ser-159 to Asn-172, Asp-196 to Phe-228, Ser-230 to His-240,Gln-253 to Gly-262, Pro-285 to Tyr-291, Pro-293 to Trp-303, Leu-310 toSer-316, Ser-321 to Arg-339.

The tissue distribution combined with the homology to a C. eleganstransmembrane-like protein indicates that the protein product of thisgene plays a role important in both vertebrates and invertegrates and isuseful for the diagnosis or treatment of disorders related to this gene.Furthermore, the tissue distribution indicates that polynucleotides andpolypeptides corresponding to this gene are useful for the diagnosisand/or treatment of hematopoietic disorders. This gene product isprimarily expressed in hematopoietic cells and tissues, suggesting thatit plays a role in the survival, proliferation, and/or differentiationof hematopoieitic lineages. This is particularly supported by theexpression of this gene product in fetal liver and bone marrow, the twoprimary sites of definitive hematopoiesis. Expression of this geneproduct in T cells and primary dendritic cells also strongly indicates arole for this protein in immune function and immune surveillance.Alternatively, the tissue distribution indicates that polynucleotidesand polypeptides corresponding to this gene are useful for thedetection, treatment, and/or prevention of various endocrine disordersand cancers, particularly Addison's disease, Cushing's Syndrome, anddisorders and/or cancers of the pancrease (e.g. diabetes mellitus),adrenal cortex, ovaries, pituitary (e.g., hyper-, hypopituitarism),thyroid (e.g. hyper-, hypothyroidism), parathyroid (e.g.hyper-,hypoparathyroidism), hypothallamus, and testes. Protein, as wellas, antibodies directed against the protein may show utility as a tumormarker and/or immunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:30 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 2012 of SEQID NO:30, b is an integer of 15 to 2026, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:30, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 21

This gene is expressed primarily in embryonic tissue, testes, and to alesser extent in ovary, hepatoma, kidney, endothelial, and smooth musclecells.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, metabolic disorder,abnormal embryonic development, or reproductive disorders, such astumors. Similarly, polypeptides and antibodies directed to thesepolypeptides are useful in providing immunological probes fordifferential identification of the tissue(s) or cell type(s). For anumber of disorders of the above tissues or cells, particularly of theembryonic or vascular tissues, expression of this gene at significantlyhigher or lower levels may be routinely detected in certain tissues orcell types (e.g., reproductive, developmental, endothelial, hepatic,renal, and cancerous and wounded tissues) or bodily fluids (e.g., lymph,amniotic fluid, bile, seminal fluid, serum, plasma, urine, synovialfluid or spinal fluid) or another tissue or cell sample taken from anindividual having such a disorder, relative to the standard geneexpression level, i.e., the expression level in healthy tissue or bodilyfluid from an individual not having the disorder.

The tissue distribution in embryonic and liver tissues, combined withthe homology to a conserved NADH dehydrogenase indicates thatpolynucleotides and polypeptides corresponding to this gene are usefulfor the diagnosis or treatment of metabolic disorders of embryonicand/or vascular tissues. Furthermore, polynucleotides and polypeptidescorresponding to this gene are useful for the diagnosis and/or treatmentof disorders of the placenta. Specific expression within the testes andovaries indicates that this gene product may play a role in the properestablishment and maintanence of normal ovarian and testicular function.Alternately, this gene product may be produced by the placenta and thentransported to the embryo, where it may play a crucial role in thedevelopment and/or survival of the developing embryo or fetus.Expression of this gene product in a vascular-rich tissue such as theplacenta also indicates that this gene product may be produced moregenerally in endothelial cells or within the circulation. In suchinstances, it may play more generalized roles in vascular function, suchas in angiogenesis. It may also be produced in the vasculature and haveeffects on other cells within the circulation, such as hematopoieticcells. It may serve to promote the proliferation, survival, activation,and/or differentiation of hematopoietic cells, as well as other cellsthroughout the body. Protein, as well as, antibodies directed againstthe protein may show utility as a tumor marker and/or immunotherapytargets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:31 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 685 of SEQID NO:31, b is an integer of 15 to 699, where both a and b correspond tothe positions of nucleotide residues shown in SEQ ID NO:31, and where bis greater than or equal to a+14.

Features of Protein Encoded by Gene No: 22

The translation product of this gene shares sequence homology with alpha1C adrenergic receptor which is thought to be important in neuronalsignal transmission. In specific embodiments, polypeptides of theinvention comprise the following amino acid sequence:TESQMKCFLGNSHDTAPRHTCSGQGLHGGXXXTAPLRALQQHSQDGKLCTNSLPAARGGPHKHVVVTVVYSVKHWKPTERSSVSIKKEEETDWDMDQLSKQRTTYEMKSGSSGVQTEELRHPSL (SEQ ID NO:181),NASWEIHMTQRHVIPXLARASMXVXXXQRPSELCSSIRRMANSAQIVFPLPVGAPTNTLSSLLYTVLNTGNQQKEAV (SEQ ID NO:182), APLRALQQHSQDGKLCTNSLPAARGGPHKH (SEQ ID NO:183),RSSVSIKKEEETDWDMDQLSKQRTTYE (SEQ ID NO:184), and/orLCSSIRRMANSAQIVFPLPVGAPTNTLSS (SEQ ID NO:185). Polynucleotides encodingthese polypeptides are also encompassed by the invention.

This gene is expressed primarily in breast lymph node, testiculartumors, and to a lesser extent, in uterine cancer.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, immune, reproductive,neural, or proliferative disorders, such as cancers. Similarly,polypeptides and antibodies directed to these polypeptides are useful inproviding immunological probes for differential identification of thetissue(s) or cell type(s). For a number of disorders of the abovetissues or cells, particularly of the neurologic, breast lymph node,uterine cancer, and testicular cancer, expression of this gene atsignificantly higher or lower levels may be routinely detected incertain tissues or cell types (e.g. breast, testes, cancerous andwounded tissues) or bodily fluids (e.g., lymph, seminal fluid, serum,plasma, urine, synovial fluid or spinal fluid) or another tissue or cellsample taken from an individual having such a disorder, relative to thestandard gene expression level, i.e., the expression level in healthytissue or bodily fluid from an individual not having the disorder.

The tissue distribution in lymph, testicular, and uterine tissuesindicates that the protein product of this gene may be beneficial in thetreatment and/or prevention of a variety of reproductive disorders, andmay even show utility in ameliorating disorders related to aberrantimmune responses to normal or proliferative tissues. The homology toalpha 1C adrenergic receptor indicates that polynucleotides andpolypeptides corresponding to this gene are useful for transmittingsignals to neurons. Furthermore, the tissue distribution indicates thatthe protein product of this gene is useful for the treatment anddiagnosis of conditions concerning proper testicular function (e.g.endocrine function, sperm maturation), as well as cancer. Therefore,this gene product is useful in the treatment of male infertility and/orimpotence. This gene product is also useful in assays designed toidentify binding agents as such agents (antagonists) are useful as malecontraceptive agents. Similarly, the protein is believed to by useful inthe treatment and/or diagnosis of testicular cancer. The testes are alsoa site of active gene expression of transcripts that may be expressed,particularly at low levels, in other tissues of the body. Therefore,this gene product may be expressed in other specific tissues or organswhere it may play related functional roles in other processes, such ashematopoiesis, inflammation, bone formation, and kidney function, toname a few possible target indications. Protein, as well as, antibodiesdirected against the protein may show utility as a tissue-specificmarker and/or immunotherapy target for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:32 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 1250 of SEQID NO:32, b is an integer of 15 to 1264, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:32, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 23

The translation product of this gene shares sequence homology withG-protein-coupled receptor which is thought to be important in mediatinga wide variety of physiological function and belongs to a genesuperfamily with members ranging from chemokine receptor to bradykininreceptor. This gene has also recently been gened by another group,calling the gene platelet activating receptor homolog. (See AccessionNo. 2580588.) Preferred polypeptide fragments comprise the amino acidsequence: LSIIFLAFVSIDRCLQL (SEQ ID NO:186),GSCFATWAFIQKNTNHRCVSIYLINLLTADFLLTLALPVKIVVDLGVAPWKLKIFHCQVTACLIYIN (SEQID NO:187), and/or KNTNHRCVSIYLINLLTADFLLTLALPVKIV (SEQ ID NO:188). Alsopreferred are polynucleotide fragments encoding these polypeptidefragments.

Chemokines, are soluble, low molecular weight members of the cytokinefamily that have chemo-attractant activity. Chemokines selectivelyinduce chemotaxis of the white blood cells, including leukocytes, suchas monocytes, macrophages, eosinophils, basophils, mast cells, andlymphocytes, such as T-cells, B-cells, and polymorphonuclear leukocytes(neutrophils). In addition, Chemokines can selectively induce otherchanges in responsive cells, including changes in cell shape, transientrises in the concentration of intracellular free calcium ([Ca2+]i),granule exocytosis, integrin upregulation, formation of bioactive lipids(e.g. leukotrienes) and respiratory burst, associated with leukocyteactivation. Therefore, the chemokines are early activators of theinflammatory response, causing inflammatory mediator release, chemotaxisand extravasation to sites of infection or inflammation.

The chemokines are related in their primary DNA structure. They sharefour conserved cysteines, which form disulphide bonds. cDNA cloning andbiochemical characterization of several chemokines has revealed theyhave a leader sequence of 20-25 amino acids, that is cleaved uponsecretion to yield a protein of approximately 92 to 99 amino acids (8 to10 Kd). The family is divided into two branches based upon the conservedcysteine motif, designated as the C—C chemokines (b chemokines) and theC—X—C chemokines (a chemokines), in which the first two conservedcysteines are adjacent, or are separated by, an intervening residue,respectively (Baggiolini, M. and C. A. Dahinden, Immunology Today,15:127-133 (1994)).

The C—X—C chemokines are potent chemoattractants and activators ofneutrophils, such as interleukin 8 (IL-8), PF4 and neutrophil-activatingpeptide 2 (NAP-2). The C—C chemokines include molecules such as humanmonocyte chemotactic proteins 1-3 (MCP-1, MCP-2, and MCP-3), RANTES(Regulated on Activation, Normal T Expressed and Secreted), and themacrophage inflammatory proteins 1a and 1b (MIP-1a and MIP-1b). The C—Cchemokines have been characterized as chemoattractants and activators ofmonocytes or lymphocytes, but do not appear to be chemoattractants forneutrophils. For example, recombinant RANTES is a chemo-attractant formonocytes, as well as, for memory T-cells in vitro (Schall, T. J. etal., Nature, 347:669-671 (1990)). Furthermore, a chemokine calledlymphotactin, with a single cysteine pair in the molecule, has beenidentified that attracts lymphocytes (Kelner, G. S., et al., Science,266:1395-1399 (1994)).

The C—C chemokines are of great scientific and pharmaceutical interestbecause of their potential role in allergic inflammation. For example,MCP-1 induces exocytosis of human basophils, resulting in release ofhigh levels of histamine and leukotriene C4, in addition to otherinflammatory mediators. Since these cellular events are triggered inresponse to chemokine binding, there remains great interest in thereceptors for the C—C chemokines. Recently, a receptor for C—Cchemokines has been gened and is reported to bind MIP-1a and RANTES.Accordingly, this MIP-1a/RANTES receptor was designated C—C chemokinereceptor 1 (CHR-1; Neote, K. et al., Cell, 72:415-425 (1993); Horuk, R.et al., WO 94/11504, published May 26, 1994; Gao, J.-I. et al. J. Exp.Med., 177: 1421-1427 (1993)). An MCP-1 receptor has also been gened(Charo, I. F. et al., Proc. Natl. Acad. Sci. USA, 91:2752 (1994)). Thisreceptor, designated CKR-2, is reported to bind MCP-1 with high affinityand MCP-3 with lower affinity (ChEO, I, F., et al., Proc. Natl. Acad.Sci. USA, 91:2752-2756 (1994)). CKR-2 has been shown to exist in twoisoforms: Isoform A and B. This dicotomy results from the use of analternative splice site in isoform A mRNA producing a distinctcytoplasmic tail. Isoform B, which is not spliced in this region, hasbeen shown to be a functional receptor for MCP-1 and MCP-3 in bothbinding and signal transduction assays (Charo, I. F. et al., Proc. Natl.Acad. Sci. USA, 91:2752-2756 (1994); Myers, S. J., et al., J. Biol.Chem., 270:5786-5792 (1995)). More recently, a new receptor called CKR-4has been described; cRNA from this receptor was reported to produce aCa2+ activated chloride current in response to MCP-1, MIP-1a and RANTESwhen injected into X. laevis oocytes (Poer, C. A., et al., J. Biol.Chem., 270: 19495-19500 (1995)). Due to the importance of Ca2+ releasein activation of signal transduction pathways in immune cells, oneexperienced in the art would appreciate the role of this receptor as theprimary initiation signal for activating subsequent signalling events.

Similarly, based upon their DNA structure, the MCP-1 receptor (CKR-2)and C—C chemokine receptor 1 are predicted to belong to a superfamily ofseven transmembrane spanning G-protein coupled receptors (Gerard C., andGerard N. P., Annu. Rev. Immunol., 12: 775-808 (1994); Gerard C., andGerard N. P., Curr. Opin. Immunol., 6:140-145 (1994)). This family ofG-protein coupled (serpentine) receptors comprises a large group ofintegral membrane proteins containing seven transmembrane-spanningregions. These regions, or domains, are believed to represent conservedtransmembrane a-helices comprising 20 to 30 hydrophobic amino acidsconnected by at least eight, divergent extracellular or cytoplasmicloops of primarily hydrophilic amino acids. Most G-protein coupledreceptors have single conserved cysteine residues on each of the firsttwo extracellular loops which form disulfide loops that are believed tostabilize functional protein structure. The seven transmembrane regionsare designated as TM1, TM2, TM3, TM4, TM5, TM6, and TM7. TM3 is alsoimplicated in signal transduction (Probst, W. C., et al., DNA and CellBiology, 11:1-20).

The ligands of these receptors include a diverse group of molecules,including small biogenic amine molecules, such as epinethrine andnorepinephrine, peptides, such as substance P and neurokinins, andlarger proteins, such as chemokines. The receptors are coupled to Gproteins, which are heterotrimeric regulatory proteins capable ofbinding GTP and mediating signal transduction from coupled receptors.For example, by the production of intracellular mediators. The ligandbinding sites of G-protein coupled receptors are believed to comprise ahydrophilic socket formed by several G-protein receptor transmembranedomains. The hydrophilic side of each G-protein coupled receptortransmembrane helix is postulated to face inward and form the polarligand binding site. TM3 has been implicated in several G-proteincoupled receptors as gaving a ligand binding site, which includes theinvolvement of the TM3 aspartate residue. Additionally, TM5 serines, aTM6 asparagine, and TM6 or TM7 phenylalanines or tyrosines are alsoimplicated in ligand binding.

It is well established that many medically significant biologicalprocesses are mediated by proteins participating in signal transductionpathways that involve G-proteins and/or second messengers, e.g. cAMP(Lefkowitz, Nature, 351:353-354 (1991)). For example, in one form ofsignal transduction, the effect of hormone binding is activation of anenzyme, adenylate cyclase, inside the cell. Enzyme activation byhormones is dependent upon the presence of the nucleotide GTP, whichitself, has been shown to influence hormone binding. A G-proteinphysically connects the hormone receptors to adenylate cyclase. Uponactivation of the hormone receptor via binding of its receptive ligand,the G-protein was shown to exchange GTP for bound GDP. The GTP-carrying,active form of the G-protein, then binds to an activated adenylatecyclase. Hydrolysis of GTP to GDP, catalyzed by the G-protein itself,returns the G-protein to its basal, inactive form. Thus, the G-proteinserves a dual role, as an intermediate that relays the signal fromreceptor to downstream effector, as well as a clock that controls theduration of the signal.

G-protein coupled receptors can be coupled intracellularly byheterotrimeric G-proteins to various intracellular enzymes, ionchannels, and transporters (Johnson, et al., Endoc., Rev., 10:317-331(1989)). Different G-protein a-subunits preferentially stimulateparticular effectors to modulate various biological functions in a cell.Phosphorylation of cytoplasmic residues of G-protein coupled receptorshave been identified as an important mechanism for the regulation ofG-protein coupling of some G-protein coupled receptors. G-proteincoupled receptors are found in numerous sites within a mammalian host,including dopamine receptors which bind to neuroleptic drugs used fortreating psychotic and neurological disorders. Other examples of membersof this family include calcitonin, adrenergic, endothelin, cAMP,adenosinse, muscarinic, acetylcholine, serotinin, histamine, thrombin,kinin, follicle stimulating hormone, opsins, endothelial differentiationgene-l receptor, and rhodopsins, odarant, cytomegalovirus receptors,etc.

Sequencing of two recently gened IL-8 receptor cDNAs have revealed thatthese C—X—C receptor proteins also share sequence similarity with seventransmembrane-spanning G protein-coupled receptor proteins (Murphy P. M.and H. L. Tiffany, Science, 253:1280-1283 (1991); Murphy et al., WO93/06299; Holmes, W. E. et al., Science, 253:1278-1290 (1991)).Additional receptors for chemotactic proteins such as anaphylatoxin C5a,and bacterial formylated tripeptide fMLP, have been characterized bycloning and found to encode receptor proteins which share sequencesimilarity to these transmembrane-spanning proteins (Gerard, N. P. andC. Gerard, Nature, 349: 614-617 (1991); Boulay, F. et al., Biochemistry,29:11123-11133 (1990)). Although a number of other proteins and geneshave been identified that share significant similarity in sequence,tissue expression, and leukocyte subpopulation distribution, to knownchemokine receptors, the ligands for these receptors remain undefined.Thus, there is a need to identify other chemokine receptor polypeptides,as these polypeptides may modulate the. Disturbances of such regulationmay be involved in disorders relating to the immune or hematopoieticsystem. Therefore, there is a need for identification andcharacterization of such human polypeptides which can play a role indetecting, preventing, ameliorating or correcting such disorders. In anattempt to express embodiments of invention via gene therapy, thefollowing protocol may be followed. Fibroblasts are obtained from asubject by skin biopsy. The resulting tissue is placed in tissue-culturemedium and separated into small pieces. Small chunks of the tissue areplaced on a wet surface of a tissue culture flask, approximately tenpieces are placed in each flask. The flask is turned upside down, closedtight and left at room temperature over night. After 24 hours at roomtemperature, the flask is inverted and the chunks of tissue remain fixedto the bottom of the flask and fresh media (e.g., Ham's F12 media, with10% FBS, penicillin and streptomycin, is added. This is then incubatedat 37° C. for approximately one week. At this time, fresh media is addedand subsequently changed every several days. After an additional twoweeks in culture, a monolayer of fibroblasts emerge. The monolayer istrypsinized and scaled into larger flasks. pMV-7 (Kirschmeier, P. T. etal, DNA, 7:219-25 (1988) flanked by the long terminal repeats of theMoloney murine sarcoma virus, is digested with EcoRI and HindIII andsubsequently treated with calf intestinal phosphatase.

The linear vector is fractionated on agarose gel and purified, usingglass beads. The cDNA encoding a polypeptide of the present invention isamplified using PCR primers which correspond to the 5′ and 3′ endsequences respectively. The 5′ primer contains an EcoRI site and the 3′primer contains a HindIII site. Equal quantities of the Moloney murinesarcoma virus linear backbone and the EcoRI and HindIII fragment areadded together, in the presence of T4 DNA ligase. The resulting mixtureis maintained under conditions appropriate for ligation of the twofragments. The ligation mixture is used to transform bacteria HB101,which are then plated onto agar-containing kanamycin for the purpose ofconfirming that the vector had the gene of interest properly inserted.The amphotropic pA317 or GP+am12 packaging cells are grown in tissueculture to confluent density in Dulbecco's Modified Eagles Medium (DMEM)with 10% calf serum (CS), penicillin and streptomycin. The MSV vectorcontaining the gene is then added to the media and the packaging cellsare transduced with the vector. The packaging cells now produceinfectious viral particles containing the gene (the packaging cells arenow referred to as producer cells).

Fresh media is added to the transduced producer cells, and subsequently,the media is harvested from a 10 cm plate of confluent producer cells.The spent media, containing the infectious viral particles, is filteredthrough a millipore filter to remove detached producer cells and thismedia is then used to infect fibroblast cells. Media is removed from asub-confluent plate of fibroblasts and quickly replaced with the mediafrom the producer cells. This media is removed and replaced with freshmedia. If the titer of virus is high, then virtually all fibroblastswill be infected and no selection is required. If the titer is very low,then it is necessary to use a retroviral vector that has a selectablemarker, such as neo or his.

The engineered fibroblasts are then injected into the host, either aloneor after having been grown to confluence on cytodex 3 microcarrierbeads. The fibroblasts now produce the protein product. Numerousmodifications and variations of the present invention are possible inlight of the above teachings and, therefore, within the scope of theappended claims, the invention may be practiced otherwise than asparticularly described.

This gene is expressed primarily in immune cells, particularlylymphocytes.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, immune orhematopoietic disorders, particularly leukemias. Similarly, polypeptidesand antibodies directed to these polypeptides are useful in providingimmunological probes for differential identification of the tissue(s) orcell type(s). For a number of disorders of the above tissues or cells,particularly of the immune system, expression of this gene atsignificantly higher or lower levels may be routinely detected incertain tissues or cell types (e.g. immune, hematopoietic, and cancerousand wounded tissues) or bodily fluids (e.g., lymph, serum, plasma,urine, synovial fluid or spinal fluid) or another tissue or cell sampletaken from an individual having such a disorder, relative to thestandard gene expression level, i.e., the expression level in healthytissue or bodily fluid from an individual not having the disorder.

Preferred epitopes include those comprising a sequence shown in SEQ IDNO:69 as residues: Asp-59 to Asn-65, Lys-72 to Trp-79, Tyr-110 toVal-121, Ala-204 to Asn-215.

The tissue distribution in immune cells, combined with the homology to aconserved G-protein coupled receptor indicates that polynucleotides andpolypeptides corresponding to this gene are useful as a chemokinereceptor on lymphocytes that regulate immune response, or may even beuseful in gene therapy to ameliorate the effects of a defectiveendogenous G-protein, or may show benefit as an antagonist for suchreceptors. The protein can also be used to determine biologicalactivity, to raise antibodies, as tissue markers, to isolate cognateligands or receptors, to identify agents that modulate theirinteractions and as nutritional supplements. It may also have a verywide range of biological activities. Typical of these are cytokine, cellproliferation/differentiation modulating activity or induction of othercytokines; immunostimulating/immunosuppressant activities (e.g. fortreating human immunodeficiency virus infection, cancer, autoimmunediseases and allergy); regulation of hematopoiesis (e.g. for treatinganaemia or as adjunct to chemotherapy); stimulation or growth of bone,cartilage, tendons, ligaments and/or nerves (e.g. for treating wounds,stimulation of follicle stimulating hormone (for control of fertility);chemotactic and chemokinetic activities (e.g. for treating infections,tumors); hemostatic or thrombolytic activity (e.g. for treatinghaemophilia, cardiac infarction etc.); anti-inflammatory activity (e.g.for treating septic shock, Crohn's disease); as antimicrobials; fortreating psoriasis or other hyperproliferative diseases; for regulationof metabolism, and behaviour. Also contemplated is the use of thecorresponding nucleic acid in gene therapy procedures. Protein, as wellas, antibodies directed against the protein may show utility as a tumormarker and/or immunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:33 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 983 of SEQID NO:33, b is an integer of 15 to 997, where both a and b correspond tothe positions of nucleotide residues shown in SEQ ID NO:33, and where bis greater than or equal to a+14.

Features of Protein Encoded by Gene No: 24

The translation product of this gene shares sequence homology withprotein disulfide isomerase which is thought to be important in proteinfolding and protein-protein interaction. This gene also contains shareshomology to genes having thioredoxin domains. (See Accession No.1943817.) This gene also maps to chromosome 9, and therefore may beuseful in linkage analysis as a marker for chromosome 9.

This gene is expressed primarily in tumor tissues.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, proliferativedisorders, or disorders involving inappropriate protein folding andprotein-protein interaction. Similarly, polypeptides and antibodiesdirected to these polypeptides are useful in providing immunologicalprobes for differential identification of the tissue(s) or cell type(s).For a number of disorders of the above tissues or cells, particularly ofthe tumorigenic process, expression of this gene at significantly higheror lower levels may be routinely detected in certain tissues or celltypes (e.g., cancerous and wounded tissues) or bodily fluids (e.g.,lymph, serum, plasma, urine, synovial fluid or spinal fluid) or anothertissue or cell sample taken from an individual having such a disorder,relative to the standard gene expression level, i.e., the expressionlevel in healthy tissue or bodily fluid from an individual not havingthe disorder.

Preferred epitopes include those comprising a sequence shown in SEQ IDNO:70 as residues: Glu-78 to Asn-83, Asp-91 to Gln-100, Glu-122 toSer-128, Arg-137 to Pro-143, Asp-157 to Asn-162, Glu-168 to Asn-174,Ser-199 to Gly-206, Pro-213 to Ala-218, Glu-251 to Thr-257, Ser-353 toHis-361, Gly-363 to Ala-375, Pro-382 to Phe-387, Arg-401 to Leu-406.

The tissue distribution in proliferative tissues, combined with thehomology to a conserved protein disulfide isomerase indicates thatpolynucleotides and polypeptides corresponding to this gene are usefulfor regulating protein folding and protein-protein interaction in tumortissues. Similarly, expression within cellular sources marked byproliferating cells indicates that this protein may play a role in theregulation of cellular division, and may show utility in the diagnosisand treatment of cancer and other proliferative disorders. Similarly,developmental tissues rely on decisions involving cell differentiationand/or apoptosis in pattern formation. Thus this protein may also beinvolved in apoptosis or tissue differentiation and could again beuseful in cancer therapy. Protein, as well as, antibodies directedagainst the protein may show utility as a tumor marker and/orimmunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:34 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 1900 of SEQID NO:34, b is an integer of 15 to 1914, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:34, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 25

In specific embodiments, polypeptides of the invention comprise thefollowing amino acid sequence: KHTVETRSVAFRKQLNR (SEQ ID NO:189).Polynucleotides encoding these polypeptides are also encompassed by theinvention.

This gene is expressed primarily in leukocytes involved in immunedefense, including T cells, macrophages, neutrophils, and to a lesserextent, in fetal liver/spleen, synovium, adrenal gland tumor, adipose,and placenta.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, immune orhematopoietic disorders, particularly defects or disorders inleukocytes. Similarly, polypeptides and antibodies directed to thesepolypeptides are useful in providing immunological probes fordifferential identification of the tissue(s) or cell type(s). For anumber of disorders of the above tissues or cells, particularly of theimmune and defense systems, expression of this gene at significantlyhigher or lower levels may be routinely detected in certain tissues orcell types (e.g. immune, hematopoietic, hepatic, reproductive,endocrine, developmental, and cancerous and wounded tissues) or bodilyfluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinalfluid) or another tissue or cell sample taken from an individual havingsuch a disorder, relative to the standard gene expression level, i.e.,the expression level in healthy tissue or bodily fluid from anindividual not having the disorder.

The tissue distribution in immune cells and tissues indicates thatpolynucleotides and polypeptides corresponding to this gene are usefulfor regulating the function of leukocytes, and is useful for thediagnosis and/or treatment of disorders in the immune and defensesystems. This gene product is primarily expressed in hematopoietic cellsand tissues, suggesting that it plays a role in the survival,proliferation, and/or differentiation of hematopoieitic lineages. Thisis particularly supported by the expression of this gene product infetal liver, which is a primary site of definitive hematopoiesis.Expression of this gene product in T cells and macrophage also stronglyindicates a role for this protein in immune function and immunesurveillance. Moreover, This gene product may be involved in theregulation of cytokine production, antigen presentation, or otherprocesses that may also suggest a usefulness in the treatment of cancer(e.g. by boosting immune responses). Since the gene is expressed incells of lymphoid origin, the natural gene product may be involved inimmune functions. Therefore it may be also used as an agent forimmunological disorders including arthritis, asthma, immunodeficiencydiseases such as AIDS, leukemia, rheumatoid arthritis, granulomatousdisease, inflammatory bowel disease, sepsis, acne, neutropenia,neutrophilia, psoriasis, hypersensitivities, such as T-cell mediatedcytotoxicity; immune reactions to transplanted organs and tissues, suchas host-versus-graft and graft-versus-host diseases, or autoimmunitydisorders, such as autoimmune infertility, lense tissue injury,demyelination, systemic lupus erythematosis, drug induced hemolyticanemia, rheumatoid arthritis, Sjogren's disease, scleroderma andtissues. In addition, this gene product may have commercial utility inthe expansion of stem cells and committed progenitors of various bloodlineages, and in the differentiation and/or proliferation of variouscell types. Protein, as well as, antibodies directed against the proteinmay show utility as a tumor marker and/or immunotherapy targets for theabove listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:35 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 1006 of SEQID NO:35, b is an integer of 15 to 1020, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:35, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 26

In specific embodiments, polypeptides of the invention comprise thefollowing amino acid sequence: PQVLHLRWLPKVLGYRSXPLRLADPSTFXM (SEQ IDNO:190),QLLGFEGNDSAGERRWRGANMQIPLLQVALPLSTEEGTGPSGPTQPSPQGEVRFLRSPRMGGQVPHWEWRSHSLPWVLTSTLSGCEGDLPGFPHQVQLPAAESHTLNTGLLRSDTGQFTPCLKLAFERPSG (SEQ IDNO:191), NDSAGERRWRGANMQIPLLQVALP (SEQ ID NO:192),PSPQGEVRFLRSPRMGGQVPHWEWRSHSL (SEQ ID NO:193), and/orHQVQLPAAESHTLNTGLLRSDTGQFTP (SEQ ID NO:194). Polynucleotides encodingthese polypeptides are also encompassed by the invention.

This gene is expressed in colon cancer, breast cancer, neutrophils, Tcells, spinal cord, fibroblasts, and vascular endothelial cells.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, gastrointesinal,reproductive, or immune disorders, particularly cancers, and disorderand abnormalities in leukocytes and other tissues. Similarly,polypeptides and antibodies directed to these polypeptides are useful inproviding immunological probes for differential identification of thetissue(s) or cell type(s). For a number of disorders of the abovetissues or cells, particularly those cells involved in tumorigenesis andimmune defense systems, expression of this gene at significantly higheror lower levels may be routinely detected in certain tissues or celltypes (e.g. immune, colon, breast, vascular, and cancerous and woundedtissues) or bodily fluids (e.g., lymph, serum, plasma, urine, synovialfluid or spinal fluid) or another tissue or cell sample taken from anindividual having such a disorder, relative to the standard geneexpression level, i.e., the expression level in healthy tissue or bodilyfluid from an individual not having the disorder.

The tissue distribution in breast and colon cancer tissues indicatesthat polynucleotides and polypeptides corresponding to this gene areuseful for diagnosis and treatment of cancer or immune system disorders.Furthermore, the tissue distribution in tumors of colon and breastorigins indicates that polynucleotides and polypeptides corresponding tothis gene are useful for diagnosis and intervention of these tumors, inaddition to other tumors where expression has been indicated.Furthermore, the protein product of this gene may be beneficial in thetreatment and/or prevention of cancers through enhancing the immuneresponse to tumor cell surface antigens, or even as a preventativethrough the correction of an aberrant cell-cycle regulator protein bygene therapy. Protein, as well as, antibodies directed against theprotein may show utility as a tissue-specific marker and/orimmunotherapy target for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:36 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 767 of SEQID NO:36, b is an integer of 15 to 781, where both a and b correspond tothe positions of nucleotide residues shown in SEQ ID NO:36, and where bis greater than or equal to a+14.

Features of Protein Encoded by Gene No: 27

The translation product of this gene shares sequence homology with amouse pancreatic polypeptide (See Accession No. 200464.). Thus, it islikely that this gene has activity similar to the mouse pancreaticpolypeptide. Preferred polypeptide fragments comprise the amino acidssequence: APLETMQNKPRAPQKRALPFPELELRDYASVLTRYSLGLRNKEPSLGHRWGTQKLGRSPC(SEQ ID NO:195),MQNKPRAPQKRALPFPELELRDYASVLTRYSLGLRNKEPSLGHRWGTQKLGRSPCSEGSQGHTTDAADVQNHSKEEQRDAGAQRXCGQGRHTWAYRXGAQDTSRLTGDPRGGERSPPKCQSMKQQEGAPSGHCWDQWCHGASEVVWPESRKRAQIFXSPCRQSPRSSALGAGQKLAVCSPDILCCPTDTLLASHPHSLLTGTQFSGQTQALAPSWCA (SEQ ID NO:196), APQKRALPFPELELRDYASVLTRYSL (SEQ ID NO:197),APQKRALPFPELELRDYASVLTRYSLG (SEQ ID NO:198),LGRSPCSEGSQGHTTDAADVQNHSKEEQR (SEQ ID NO:199), and/orTDTLLASHPHSLLTGTQFSGQTQAL (SEQ ID NO:200). Also preferred arepolynucleotide fragments encoding this polypeptide fragment.

This gene is expressed primarily in neutrophils, and to a lesser extent,in induced endothelial cells.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, immune, hematopoietic,or vascular disorders, particularly disorders in immune cell adhesion.Similarly, polypeptides and antibodies directed to these polypeptidesare useful in providing immunological probes for differentialidentification of the tissue(s) or cell type(s). For a number ofdisorders of the above tissues or cells, particularly of the immunesystem, expression of this gene at significantly higher or lower levelsmay be routinely detected in certain tissues or cell types (e.g. immune,vascular, and cancerous and wounded tissues) or bodily fluids (e.g.lymph, serum, plasma, urine, synovial fluid or spinal fluid) or anothertissue or cell sample taken from an individual having such a disorder,relative to the standard gene expression level, i.e., the expressionlevel in healthy tissue or bodily fluid from an individual not havingthe disorder.

The tissue distribution in neutrophils and endothelial cells indicatesthat polynucleotides and polypeptides corresponding to this gene areuseful for the regulation of neutrophils or leukocyte adhesion toendothelial cells. It may be used to diagnose or treat disordersassociated with neutrophils and vascular endothelial cells. Furthermore,this gene product may be produced more generally in endothelial cells orwithin the circulation. In such instances, it may play more generalizedroles in vascular function, such as in angiogenesis. It may also beproduced in the vasculature and have effects on other cells within thecirculation, such as hematopoietic cells, or be used as a preventativefor embolisms, atherosclerosis, aneurysms, microvascular disease, orstroke. It may serve to promote the proliferation, survival, activation,and/or differentiation of hematopoietic cells, as well as other cellsthroughout the body. Protein, as well as, antibodies directed againstthe protein may show utility as a tumor marker and/or immunotherapytargets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:37 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 952 of SEQID NO:37, b is an integer of 15 to 966, where both a and b correspond tothe positions of nucleotide residues shown in SEQ ID NO:37, and where bis greater than or equal to a+14.

Features of Protein Encoded by Gene No: 28

In specific embodiments, polypeptides of the invention comprise thefollowing amino acid sequence:IAQVLKAEMCLVXRPHPXLLDSHRGWAGETLRGQGRQEXESDTKAGTLQLQRQAPLPLTQHSLVLPISPGPSNHTQS (SEQ ID NO:201), RGWAGETLRGQGRQEXESDT (SEQ ID NO:202), and/orAPLPLTQHSLVLPISPGPSN (SEQ ID NO:203). Polynucleotides encoding thesepolypeptides are also encompassed by the invention.

This gene is expressed primarily in prostate BPH.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, proliferative orreproductive disorders, particularly benign hypertrophy of the prostate.Similarly, polypeptides and antibodies directed to these polypeptidesare useful in providing immunological probes for differentialidentification of the tissue(s) or cell type(s). For a number ofdisorders of the above tissues or cells, particularly of the maleurogenital system, expression of this gene at significantly higher orlower levels may be routinely detected in certain tissues or cell types(e.g. prostate, urogenital, and cancerous and wounded tissues) or bodilyfluids (e.g., lymph, serum, plasma, urine, synovial fluid or spinalfluid) or another tissue or cell sample taken from an individual havingsuch a disorder, relative to the standard gene expression level, i.e.,the expression level in healthy tissue or bodily fluid from anindividual not having the disorder.

The tissue distribution in prostate tissue indicates thatpolynucleotides and polypeptides corresponding to this gene are usefulfor the diagnosis and treatment of benign or metastatic hypertrophy ofthe prostate or prostate cancer. Expression within cellular sourcesmarked by proliferating cells indicates that this protein may play arole in the regulation of cellular division, and may show utility in thediagnosis and treatment of cancer and other proliferative disorders.Similarly, developmental tissues rely on decisions involving celldifferentiation and/or apoptosis in pattern formation. Thus this proteinmay also be involved in apoptosis or tissue differentiation and couldagain be useful in cancer therapy. Protein, as well as, antibodiesdirected against the protein may show utility as a tumor marker and/orimmunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:38 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 402 of SEQID NO:38, b is an integer of 15 to 416, where both a and b correspond tothe positions of nucleotide residues shown in SEQ ID NO:38, and where bis greater than or equal to a+14.

Features of Protein Encoded by Gene No: 29

The translation product of this gene shares sequence homology withC16C10.7, a C. elegans gene similar to zinc finger protein, a proteininvolved in DNA binding. Thus, this protein is expected to share certainbiological activities with C1610.7 including DNA binding activities. Oneembodiment of this gene comprises polypeptides of the following aminoacid sequence:NRERGGAGATFECNICLETAREAVVSVCGHLYCWPCLHQWLETRPERQECPVCKAGISREKVVPLYGRGSQKPQDPRLKTPPRPQGQRPAPESRGGFQPFGDTGGFHFSFGVGAFPFGFFTTVFNAHEPFRRGTGVDLGQGHPASSWQDSLFLFLAIFFFFWLLSI (SEQ ID NO:204),NRERGGAGATFECNICLETAREAVVSVCGHLYCWPCLHQWLETRPERQECPVCKAGISREKVVPLYGRGSQKPQDPRLKTPPRPQGQRPAPESRGGFQPFGDTGGFHFSFGVGAFPFGFFTTVFNAHEPFRRGTGVDLGQGHPASSWQD (SEQ ID NO:205), NRERGGAGATFECNICLETAREAVVSVCGHLYCWPCLHQWL (SEQID NO:206), ETRPERQECPVCKAGISREKVVPLYGRGSQKPQDPRLK (SEQ ID NO:207),TPPRPQGQRPAPESRGGFQPFGDTGGFHFSFGVG (SEQ ID NO:208),AFPFGFFTTVFNAHEPFRRGTGVDLGQGHPASSWQD (SEQ ID NO:209). An additionalembodiment is the polynucleotides encoding these polypeptides.

This gene is expressed primarily in activated T-cells, and to a lesserextent, in fetal brain, TNF-induced amniotic cells and epididymus.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, immune,neurodegenerative, or developmental disorders. Similarly, polypeptidesand antibodies directed to these polypeptides are useful in providingimmunological probes for differential identification of the tissue(s) orcell type(s). For a number of disorders of the above tissues or cells,particularly of the immune and central nervous systems, expression ofthis gene at significantly higher or lower levels may be routinelydetected in certain tissues or cell types (e.g. immune, neural,developmental, reproductive, and cancerous and wounded tissues) orbodily fluids (e.g., lymph, amniotic fluid, seminal fluid, serum,plasma, urine, synovial fluid or spinal fluid) or another tissue or cellsample taken from an individual having such a disorder, relative to thestandard gene expression level, i.e., the expression level in healthytissue or bodily fluid from an individual not having the disorder.

The tissue distribution in T-cells and fetal brain indicates that theprotein products of this gene are useful for the diagnosis and treatmentof immune and/or neurodegenerative disorders, as well as useful for thepromotion of, survival, and differentiation of neurons. Furthermore, thetissue distribution indicates that polynucleotides and polypeptidescorresponding to this gene are useful for the diagnosis and/or treatmentof hematopoietic disorders. Expression of this gene product in T cellsalso strongly indicates a role for this protein in immune function andimmune surveillance. Expression within embryonic tissue and othercellular sources marked by proliferating cells indicates that thisprotein may play a role in the regulation of cellular division, and mayshow utility in the diagnosis and treatment of cancer and otherproliferative disorders. Similarly, developmental tissues rely ondecisions involving cell differentiation and/or apoptosis in patternformation. Thus this protein may also be involved in apoptosis or tissuedifferentiation and could again be useful in cancer therapy. Protein, aswell as, antibodies directed against the protein may show utility as atumor marker and/or immunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:39 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 1100 of SEQID NO:39, b is an integer of 15 to 1114, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:39, and whereb is greater than or equal to a+14.

Features of Protein Encoded by Gene No: 30

In specific embodiments, polypeptides of the invention comprise thefollowing amino acid sequence: GLSTGPDMASLDLFV (SEQ ID NO:210),GRPTRPSQATRHFLLGTLFTNCLCGTFCFPCLGCQVAADMNECCLCGTSVAMRTLYRTRYGIPGSICDDYMATLCCPHCTLCQIKRDINRRRATF (SEQ ID NO:211),IKNLIFFMPSVVLKHIHHISVAKDGEELKLKRCLLNFVASVRAFHHQFLESTHGSPSVDISLDLAKSTMRTAKSCHIVITNRSRDAISGPVESPHCDACSTQTAFIHISCNLTPKARETKCATETISKQGSEQEMSCGLGRTRGST(SEQ ID NO:212), FLLGTLFTNCLCGTFCFPCLGCQ (SEQ ID NO:213),SICDDYMATLCCPHCTLCQIKRDI (SEQ ID NO:214), SVVLKHIHMMSVAKDGEELKLKRCLLNFVA(SEQ ID NO:215), NFVASVRAFHHQFLESTHGSPSVDIS (SEQ ID NO:216), and/orTAFIHISCNLTPKARETKCATETISKQG (SEQ ID NO:217). Polynucleotides encodingthese polypeptides are also encompassed by the invention. The geneencoding the disclosed cDNA is thought to reside on chromosome 4.Accordingly, polynucleotides related to this invention are useful as amarker in linkage analysis for chromosome 4.

This gene is expressed primarily in T-cells, fetal tissues, andplacenta, and to a lesser extent in bone marrow.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, immunological,developmental, or reproductive disorders, including autoimmune diseasesor congenital defects. Similarly, polypeptides and antibodies directedto these polypeptides are useful in providing immunological probes fordifferential identification of the tissue(s) or cell type(s). For anumber of disorders of the above tissues or cells, particularly of theimmune system, expression of this gene at significantly higher or lowerlevels may be routinely detected in certain tissues or cell types (e.g.immune, developmental, placental, hematopoietic, and cancerous andwounded tissues) or bodily fluids (e.g. lymph, serum, plasma, urine,synovial fluid or spinal fluid) or another tissue or cell sample takenfrom an individual having such a disorder, relative to the standard geneexpression level, i.e., the expression level in healthy tissue or bodilyfluid from an individual not having the disorder.

The tissue distribution in T-cells and bone marrow indicates that theprotein products of this gene are useful for diagnosis and treatment ofimmunologically mediated disorders as they are thought to play a role inthe proliferation, survival, differentiation, and/or activation of avariety of hematopoietic cells, including early progenitors orhematopoietic stem cells. Furthermore, the tissue distribution indicatesthat polynucleotides and polypeptides corresponding to this gene areuseful for the diagnosis and treatment of cancer and other proliferativedisorders. Expression within embryonic tissue and other cellular sourcesmarked by proliferating cells indicates that this protein may play arole in the regulation of cellular division. Additionally, theexpression in hematopoietic cells and tissues indicates that thisprotein may play a role in the proliferation, differentiation, and/orsurvival of hematopoietic cell lineages. In such an event, this gene maybe useful in the treatment of lymphoproliferative disorders, and in themaintenance and differentiation of various hematopoietic lineages fromearly hematopoietic stem and committed progenitor cells. Similarly,embryonic development also involves decisions involving celldifferentiation and/or apoptosis in pattern formation. Thus, thisprotein may also be involved in apoptosis or tissue differentiation andcould again be useful in cancer therapy. Protein, as well as, antibodiesdirected against the protein may show utility as a tumor marker and/orimmunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:40 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 588 of SEQID NO:40, b is an integer of 15 to 602, where both a and b correspond tothe positions of nucleotide residues shown in SEQ ID NO:40, and where bis greater than or equal to a+14.

Features of Protein Encoded by Gene No: 31

In specific embodiments, polypeptides of the invention comprise thefollowing amino acid sequence: MKGEIE (SEQ ID NO:218). Polynucleotidesencoding these polypeptides are also encompassed by the invention.

This gene is expressed primarily in human skin, and to a lesser extent,in fetal heart tissue.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, integumentary,developmental, or cardiovascular disorders, particularly wound healingconditions and skin cancers. Similarly, polypeptides and antibodiesdirected to these polypeptides are useful in providing immunologicalprobes for differential identification of the tissue(s) or cell type(s).For a number of disorders of the above tissues or cells, particularly ofthe integumentary system, expression of this gene at significantlyhigher or lower levels may be routinely detected in certain tissues orcell types (e.g. skin, developmental, cardiovascular, and cancerous andwounded tissues) or bodily fluids (e.g., lymph, serum, plasma, urine,synovial fluid or spinal fluid) or another tissue or cell sample takenfrom an individual having such a disorder, relative to the standard geneexpression level, i.e., the expression level in healthy tissue or bodilyfluid from an individual not having the disorder.

The tissue distribution in skin indicates that the protein products ofthis gene are useful for diagnosis and treatment of skin cancers andwound healing. Moreover, polynucleotides and polypeptides correspondingto this gene are useful for the treatment, diagnosis, and/or preventionof various skin disorders including congenital disorders (i.e. nevi,moles, freckles, Mongolian spots, hemangiomas, port-wine syndrome),integumentary tumors (i.e. keratoses, Bowen's disease, basal cellcarcinoma, squamous cell carcinoma, malignant melanoma, Paget's disease,mycosis fungoides, and Kaposi's sarcoma), injuries and inflammation ofthe skin (i.e. wounds, rashes, prickly heat disorder, psoriasis,dermatitis), atherosclerosis, uticaria, eczema, photosensitivity,autoimmune disorders (i.e. lupus erythematosus, vitiligo,dermatomyositis, morphea, scleroderma, pemphigoid, and pemphigus),keloids, striae, erythema, petechiae, purpura, and xanthelasma. Inaddition, such disorders may predispose increased susceptibility toviral and bacterial infections of the skin (i.e. cold sores, warts,chickenpox, molluscum contagiosum, herpes zoster, boils, cellulitis,erysipelas, impetigo, tinea, athletes foot, and ringworm).

Moreover, the protein product of this gene may also be useful for thetreatment or diagnosis of various connective tissue disorders such asarthritis, trauma, tendonitis, chrondomalacia and inflammation,autoimmune disorders such as rheumatoid arthritis, lupus, scleroderma,and dermatomyositis as well as dwarfism, spinal deformation, andspecific joint abnormalities as well as chondrodysplasias (i.e.spondyloepiphyseal dysplasia congenita, familial osteoarthritis,Atelosteogenesis type II, metaphyseal chondrodysplasia type Schmid).Additionally, it may play more generalized roles in vascular function,such as in angiogenesis. It may also be produced in the vasculature andhave effects on other cells within the circulation, such ashematopoietic cells. It may serve to promote the proliferation,survival, activation, and/or differentiation of hematopoietic cells, aswell as other cells throughout the body. Protein, as well as, antibodiesdirected against the protein may show utility as a tumor marker and/orimmunotherapy targets for the above listed tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:41 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 956 of SEQID NO:41, b is an integer of 15 to 970, where both a and b correspond tothe positions of nucleotide residues shown in SEQ ID NO:41, and where bis greater than or equal to a+14.

Features of Protein Encoded by Gene No: 32

The translation product of this gene shares sequence homology with humanTear Prealbumin (GenBank accession no. gi|307518) and ratOderant-binding protein (GenBank accession no. gi|207551), both of whichare thought to be important in molecule binding and transport. Thetranslation product of this gene is a homolog of the lipocalin family,which are thought to be involved in the transport of small hydrophobicmolecules. In specific embodiments, polypeptides of the inventioncomprise the following amino acid sequence: EFGTSRGRQHRALE (SEQ IDNO:219),HQTPGVTGLSAVEMDQITPALWEALAIDTLRKLRIGTRRPRIRWGQEAHVPAGAAQEGPLHLLLQRPAPWGXAPHGKACG (SEQ ID NO:220),GLGQGGQGLDGGRKLMYLQELPRRDHYEFYCKDQHHGGXLHMGKLVGRNSDTNREALEEFKKLVQRKGLSEEDIFTPLQTGSCVPEH (SEQ ID NO:221),SGPSRLRTSLSHPVSDVRATSPPGRRGQPLLGGGQSWGPGKRAAWALSTCGGWCTGVGGGGXWGWEWGRGSQALYLPGSSVFRXRIFFWMHRSSLMKVNVASNFPPPRAVTFTGDTFWASCLRKVLSTTMAFTYQVPVISSSXRVKDRAAAXPSVTPRNRVFISRALCCRPRLVPN (SEQ ID NO:222),GLPEGRRDLVHLDCGQACHTRCLMSGPPAPQEGEASPSLEVGRAGALAKGQPGHSLPVEAGALGLAVGEGGGGXGGGAHRRCICQAPPSSAXGFSSGCTDPPS (SEQ ID NO:223),VEMDQITPALWEALAIDTLRKLRIGTRRPR (SEQ ID NO:224), RKLMYLQELPRRDHYIFYCKDQH(SEQ ID NO:225), EALEEFKKLVQRKGLSEEDIFTP (SEQ ID NO:226),RATSPPGRRGQPLLGGGQSWGPGKRAA (SEQ ID NO:227),FFWMHRSSLMKVNVASNFPPPRAVTFTGD (SEQ ID NO:228), and/orCLMSGPPAPQEGEASPSLEVGRAGALAK (SEQ ID NO:229). Polynucleotides encodingthese polypeptides are also encompassed by the invention.

This gene is expressed primarily in endometrial tumor.

Therefore, polynucleotides and polypeptides of the invention are usefulas reagents for differential identification of the tissue(s) or celltype(s) present in a biological sample and for diagnosis of diseases andconditions which include, but are not limited to, reproductivedisorders, particularly cancers of the endometrium, skin andhaemopoietic system. Similarly, polypeptides and antibodies directed tothese polypeptides are useful in providing immunological probes fordifferential identification of the tissue(s) or cell type(s). For anumber of disorders of the above tissues or cells, particularly of thehaemopoietic system, expression of this gene at significantly higher orlower levels may be routinely detected in certain tissues or cell types(e.g. immune, reproductive, and cancerous and wounded tissues) or bodilyfluids (e.g., lymph, serum, amniotic fluid, plasma, urine, synovialfluid or spinal fluid) or another tissue or cell sample taken from anindividual having such a disorder, relative to the standard geneexpression level, i.e., the expression level in healthy tissue or bodilyfluid from an individual not having the disorder.

The tissue distribution in endometrium tissue, combined with thehomology to the molecule binding and transport gene family indicatesthat the protein products of this gene are useful for the diagnosis andtreatment of cancers of the endometrium and haemopoietic system as wellas for the treatment of autoimmune disorders such as inflammation.Protein, as well as, antibodies directed against the protein may showutility as a tumor marker and/or immunotherapy targets for the abovelisted tissues.

Many polynucleotide sequences, such as EST sequences, are publiclyavailable and accessible through sequence databases. Some of thesesequences are related to SEQ ID NO:42 and may have been publiclyavailable prior to conception of the present invention. Preferably, suchrelated polynucleotides are specifically excluded from the scope of thepresent invention. To list every related sequence is cumbersome.Accordingly, preferably excluded from the present invention are one ormore polynucleotides comprising a nucleotide sequence described by thegeneral formula of a−b, where a is any integer between 1 to 988 of SEQID NO:42, b is an integer of 15 to 1002, where both a and b correspondto the positions of nucleotide residues shown in SEQ ID NO:42, and whereb is greater than or equal to a+14. TABLE 1 5′ NT First Last ATCC NT 5′NT 3′ NT of First AA AA AA First AA Deposit SEQ Total of of 5′ NT AA ofSEQ of of of Last Gene cDNA Nr and ID NT Clone Clone of Start Signal IDSig Sig Secreted AA of No. Clone ID Date Vector NO: X Seq. Seq. Seq.Codon Pep NO: Y Pep Pep Portion ORF 1 HSVBZ80  97978 Uni-ZAP XR 11 116964 1060 162 162 47 1 38 39 145 Mar. 27, 1997 209075 May 22, 1997 2HTAAU21  97978 Uni-ZAP XR 12 1310 1 1310 283 283 48 1 18 19 311 Mar. 27,1997 209075 May 22, 1997 3 HTLEK16  97978 Uni-ZAP XR 13 1139 19 1111 25149 1 21 22 46 Mar. 27, 1997 209075 May 22, 1997 4 HUSIR91  97978 pSport114 2271 743 2271 59 59 50 1 23 24 467 Mar. 27, 1997 209075 May 22, 19974 HUSIR91  97978 pSport1 43 2581 1035 2164 1148 1148 79 1 27 28 207 Mar.27, 1997 209075 May 22, 1997 5 HADMC21  97978 pBluescript 15 626 60 47991 91 51 1 51 52 82 Mar. 27, 1997 209075 May 22, 1997 6 HAGFM45  97978Uni-ZAP XR 16 2118 1170 2058 1248 1248 52 1 16 17 62 Mar. 27, 1997209075 May 22, 1997 7 HAIBE65  97978 Uni-ZAP XR 17 1076 396 993 528 52853 1 31 32 123 Mar. 27, 1997 209075 May 22, 1997 8 HAQBH57  97978Uni-ZAP XR 18 1379 420 1306 618 618 54 1 25 26 179 Mar. 27, 1997 209075May 22, 1997 9 HATCX80  97978 Uni-ZAP XR 19 1337 47 1337 199 199 55 1 1819 286 Mar. 27, 1997 209075 May 22, 1997 10 HCFLQ84  97978 pSport1 201390 237 1390 410 410 56 1 20 21 33 Mar. 27, 1997 209075 May 22, 1997 11HCFLS78  97978 pSport1 21 1431 178 981 420 420 57 1 21 22 23 Mar. 27,1997 209075 May 22, 1997 12 HTADI12  97978 Uni-ZAP XR 22 2539 69 2539104 104 58 1 27 28 46 Mar. 27, 1997 209075 May 22, 1997 13 HEMCM42 97978 Uni-ZAP XR 23 1041 48 1007 58 58 59 1 29 30 113 Mar. 27, 1997209075 May 22, 1997 14 HEONP72  97978 pSport1 24 1962 1 1947 181 181 601 19 20 31 Mar. 27, 1997 209075 May 22, 1997 15 HFCDW34  97978 Uni-ZAPXR 25 1228 321 1228 525 525 61 1 24 25 80 Mar. 27, 1997 209075 May 22,1997 16 HTTEU91  97978 Uni-ZAP XR 26 1340 325 1340 15 15 62 1 18 19 104Mar. 27, 1997 209075 May 22, 1997 17 HHGBF89  97978 Lambda ZAP II 27 80631 806 77 77 63 1 19 20 145 Mar. 27, 1997 209075 May 22, 1997 17 HHGBF89 97978 Lambda ZAP II 44 796 31 796 77 77 80 1 25 26 145 Mar. 27, 1997209075 May 22, 1997 18 HKIYQ65  97978 pBluescript 28 696 1 684 98 98 641 17 18 30 Mar. 27, 1997 209075 May 22, 1997 19 HKMLN27  97978pBluescript 29 1007 71 963 129 129 65 1 23 24 259 Mar. 27, 1997 209075May 22, 1997 20 HKIAC30 209022 Uni-ZAP XR 30 2026 131 2018 166 166 66 130 31 339 May 08, 1997 20 HKIAC30 209022 Uni-ZAP XR 45 2017 126 2007 161161 81 1 22 May 08, 1997 21 HKIXB95 209022 pBluescript 31 699 196 699230 230 67 1 22 23 26 May 08, 1997 22 HLMIY86 209022 Lambda ZAP II 321264 1 1264 560 560 68 1 24 25 76 May 08, 1997 23 HLYAZ61 209022 pSport133 997 74 997 205 205 69 1 20 21 215 May 08, 1997 24 HMQDT36 209022Uni-ZAP XR 34 1914 37 1897 192 192 70 1 32 33 406 May 08, 1997 25HNEDF25 209022 Uni-ZAP XR 35 1020 1 1010 210 210 71 1 13 14 45 May 08,1997 26 HNFET17 209022 Uni-ZAP XR 36 781 31 781 100 100 72 1 33 May 08,1997 27 HNHCR46 209022 Uni-ZAP XR 37 966 19 460 458 458 73 1 24 25 160May 08, 1997 28 HPWAS91 209022 Uni-ZAP XR 38 416 1 416 95 95 74 1 24 2525 May 08, 1997 29 HWTAW41 209022 Uni-ZAP XR 39 1114 804 1114 50 50 75 143 44 91 May 08, 1997 30 HBMUT52 209022 Uni-ZAP XR 40 602 142 602 204204 76 1 26 27 32 May 08, 1997 31 HERAG83 209022 Uni-ZAP XR 41 970 1 970110 110 77 1 22 23 22 May 08, 1997 32 HETFI51 209022 Uni-ZAP XR 42 10021 1002 43 43 78 1 21 22 173 May 08, 1997 32 HETFI51 209022 Uni-ZAP XR 46981 1 981 23 23 82 1 17 18 30 May 08, 1997

Table 1 summarizes the information corresponding to each “Gene No.”described above. The nucleotide sequence identified as “NT SEQ ID NO:X”was assembled from partially homologous (“overlapping”) sequencesobtained from the “cDNA clone ID” identified in Table 1 and, in somecases, from additional related DNA clones. The overlapping sequenceswere assembled into a single contiguous sequence of high redundancy(usually three to five overlapping sequences at each nucleotideposition), resulting in a final sequence identified as SEQ ID NO:X.

The cDNA Clone ID was deposited on the date and given the correspondingdeposit number listed in “ATCC Deposit No: Z and Date.” Some of thedeposits contain multiple different clones corresponding to the samegene. “Vector” refers to the type of vector contained in the cDNA CloneID.

“Total NT Seq.” refers to the total number of nucleotides in the contigidentified by “Gene No.” The deposited clone may contain all or most ofthese sequences, reflected by the nucleotide position indicated as “5′NT of Clone Seq.” and the “3′ NT of Clone Seq.” of SEQ ID NO:X. Thenucleotide position of SEQ ID NO:X of the putative start codon(methionine) is identified as “5′ NT of Start Codon.” Similarly, thenucleotide position of SEQ ID NO:X of the predicted signal sequence isidentified as “5′ NT of First AA of Signal Pep.”

The translated amino acid sequence, beginning with the methionine, isidentified as “AA SEQ ID NO:Y,” although other reading frames can alsobe easily translated using known molecular biology techniques. Thepolypeptides produced by these alternative open reading frames arespecifically contemplated by the present invention.

The first and last amino acid position of SEQ ID NO:Y of the predictedsignal peptide is identified as “First AA of Sig Pep” and “Last AA ofSig Pep.” The predicted first amino acid position of SEQ ID NO:Y of thesecreted portion is identified as “Predicted First AA of SecretedPortion.” Finally, the amino acid position of SEQ ID NO:Y of the lastamino acid in the open reading frame is identified as “Last AA of ORF.”

SEQ ID NO:X and the translated SEQ ID NO:Y are sufficiently accurate andotherwise suitable for a variety of uses well known in the art anddescribed further below. For instance, SEQ ID NO:X is useful fordesigning nucleic acid hybridization probes that will detect nucleicacid sequences contained in SEQ ID NO:X or the cDNA contained in thedeposited clone. These probes will also hybridize to nucleic acidmolecules in biological samples, thereby enabling a variety of forensicand diagnostic methods of the invention. Similarly, polypeptidesidentified from SEQ ID NO:Y may be used to generate antibodies whichbind specifically to the secreted proteins encoded by the EDNA clonesidentified in Table 1.

Nevertheless, DNA sequences generated by sequencing reactions cancontain sequencing errors. The errors exist as misidentifiednucleotides, or as insertions or deletions of nucleotides in thegenerated DNA sequence. The erroneously inserted or deleted nucleotidescause frame shifts in the reading frames of the predicted amino acidsequence. In these cases, the predicted amino acid sequence divergesfrom the actual amino acid sequence, even though the generated DNAsequence may be greater than 99.9% identical to the actual DNA sequence(for example, one base insertion or deletion in an open reading frame ofover 1000 bases).

Accordingly, for those applications requiring precision in thenucleotide sequence or the amino acid sequence, the present inventionprovides not only the generated nucleotide sequence identified as SEQ IDNO:X and the predicted translated amino acid sequence identified as SEQID NO:Y, but also a sample of plasmid DNA containing a human cDNA of theinvention deposited with the ATCC, as set forth in Table 1. Thenucleotide sequence of each deposited clone can readily be determined bysequencing the deposited clone in accordance with known methods. Thepredicted amino acid sequence can then be verified from such deposits.Moreover, the amino acid sequence of the protein encoded by a particularclone can also be directly determined by peptide sequencing or byexpressing the protein in a suitable host cell containing the depositedhuman cDNA, collecting the protein, and determining its sequence.

The present invention also relates to the genes corresponding to SEQ IDNO:X, SEQ ID NO:Y, or the deposited clone. The corresponding gene can beisolated in accordance with known methods using the sequence informationdisclosed herein. Such methods include preparing probes or primers fromthe disclosed sequence and identifying or amplifying the correspondinggene from appropriate sources of genomic material.

Also provided in the present invention are species homologs. Specieshomologs may be isolated and identified by making suitable probes orprimers from the sequences provided herein and screening a suitablenucleic acid source for the desired homologue.

The polypeptides of the invention can be prepared in any suitablemanner. Such polypeptides include isolated naturally occurringpolypeptides, recombinantly produced polypeptides, syntheticallyproduced polypeptides, or polypeptides produced by a combination ofthese methods. Means for preparing such polypeptides are well understoodin the art.

The polypeptides may be in the form of the secreted protein, includingthe mature form, or may be a part of a larger protein, such as a fusionprotein (see below). It is often advantageous to include an additionalamino acid sequence which contains secretory or leader sequences,pro-sequences, sequences which aid in purification, such as multiplehistidine residues, or an additional sequence for stability duringrecombinant production.

The polypeptides of the present invention are preferably provided in anisolated form, and preferably are substantially purified. Arecombinantly produced version of a polypeptide, including the secretedpolypeptide, can be substantially purified by the one-step methoddescribed in Smith and Johnson, Gene 67:31-40 (1988). Polypeptides ofthe invention also can be purified from natural or recombinant sourcesusing antibodies of the invention raised against the secreted protein inmethods which are well known in the art.

Signal Sequences

Methods for predicting whether a protein has a signal sequence, as wellas the cleavage point for that sequence, are available. For instance,the method of McGeoch, Virus Res. 3:271-286 (1985), uses the informationfrom a short N-terminal charged region and a subsequent uncharged regionof the complete (uncleaved) protein. The method of von Heinje, NucleicAcids Res. 14:4683-4690 (1986) uses the information from the residuessurrounding the cleavage site, typically residues −13 to +2, where +1indicates the amino terminus of the secreted protein. The accuracy ofpredicting the cleavage points of known mammalian secretory proteins foreach of these methods is in the range of 75-80%. (von Heinje, supra.)However, the two methods do not always produce the same predictedcleavage point(s) for a given protein.

In the present case, the deduced amino acid sequence of the secretedpolypeptide was analyzed by a computer program called SignalP (HenrikNielsen et al., Protein Engineering 10:1-6 (1997)), which predicts thecellular location of a protein based on the amino acid sequence. As partof this computational prediction of localization, the methods of McGeochand von Heinje are incorporated. The analysis of the amino acidsequences of the secreted proteins described herein by this programprovided the results shown in Table 1.

As one of ordinary skill would appreciate, however, cleavage sitessometimes vary from organism to organism and cannot be predicted withabsolute certainty. Accordingly, the present invention provides secretedpolypeptides having a sequence shown in SEQ ID NO:Y which have anN-terminus beginning within 5 residues (i.e., + or −5 residues) of thepredicted cleavage point. Similarly, it is also recognized that in somecases, cleavage of the signal sequence from a secreted protein is notentirely uniform, resulting in more than one secreted species. Thesepolypeptides, and the polynucleotides encoding such polypeptides, arecontemplated by the present invention.

Moreover, the signal sequence identified by the above analysis may notnecessarily predict the naturally occurring signal sequence. Forexample, the naturally occurring signal sequence may be further upstreamfrom the predicted signal sequence. However, it is likely that thepredicted signal sequence will be capable of directing the secretedprotein to the ER. These polypeptides, and the polynucleotides encodingsuch polypeptides, are contemplated by the present invention.

Polynucleotide and Polypeptide Variants

“Variant” refers to a polynucleotide or polypeptide differing from thepolynucleotide or polypeptide of the present invention, but retainingessential properties thereof. Generally, variants are overall closelysimilar, and, in many regions, identical to the polynucleotide orpolypeptide of the present invention.

By a polynucleotide having a nucleotide sequence at least, for example,95% “identical” to a reference nucleotide sequence of the presentinvention, it is intended that the nucleotide sequence of thepolynucleotide is identical to the reference sequence except that thepolynucleotide sequence may include up to five point mutations per each100 nucleotides of the reference nucleotide sequence encoding thepolypeptide. In other words, to obtain a polynucleotide having anucleotide sequence at least 95% identical to a reference nucleotidesequence, up to 5% of the nucleotides in the reference sequence may bedeleted or substituted with another nucleotide, or a number ofnucleotides up to 5% of the total nucleotides in the reference sequencemay be inserted into the reference sequence. The query sequence may bean entire sequence shown in Table 1, the ORF (open reading frame), orany fragment specified as described herein.

As a practical matter, whether any particular nucleic acid molecule orpolypeptide is at least 90%, 95%, 96%, 97%, 98% or 99% identical to anucleotide sequence of the presence invention can be determinedconventionally using known computer programs. A preferred method fordeterming the best overall match between a query sequence (a sequence ofthe present invention) and a subject sequence, also referred to as aglobal sequence alignment, can be determined using the FASTDB computerprogram based on the algorithm of Brutlag et al. (Comp. App. Biosci.(1990) 6:237-245). In a sequence alignment the query and subjectsequences are both DNA sequences. An RNA sequence can be compared byconverting U's to T's. The result of said global sequence alignment isin percent identity. Preferred parameters used in a FASTDB alignment ofDNA sequences to calculate percent identify are: Matrix=Unitary,k-tuple=4, Mismatch Penalty=1, Joining Penalty=30, Randomization GroupLength=0, Cutoff Score=1, Gap Penalty=5, Gap Size Penalty 0.05, WindowSize=500 or the length of the subject nucleotide sequence, whichever isshorter.

If the subject sequence is shorter than the query sequence because of 5′or 3′ deletions, not because of internal deletions, a manual correctionmust be made to the results. This is because the FASTDB program does notaccount for 5′ and 3′ truncations of the subject sequence whencalculating percent identity. For subject sequences truncated at the 5′or 3′ ends, relative to the the query sequence, the percent identity iscorrected by calculating the number of bases of the query sequence thatare 5′ and 3′ of the subject sequence, which are not matched/aligned, asa percent of the total bases of the query sequence. Whether a nucleotideis matched/aligned is determined by results of the FASTDB sequencealignment. This percentage is then subtracted from the percent identity,calculated by the above FASTDB program using the specified parameters,to arrive at a final percent identity score. This corrected score iswhat is used for the purposes of the present invention. Only basesoutside the 5′ and 3′ bases of the subject sequence, as displayed by theFASTDB alignment, which are not matched/aligned with the query sequence,are calculated for the purposes of manually adjusting the percentidentity score.

For example, a 90 base subject sequence is aligned to a 100 base querysequence to determine percent identity. The deletions occur at the 5′end of the subject sequence and therefore, the FASTDB alignment does notshow a matched/alignment of the first 10 bases at 5′ end. The 10unpaired bases represent 10% of the sequence (number of bases at the 5′and 3′ ends not matched/total number of bases in the query sequence) so10% is subtracted from the percent identity score calculated by theFASTDB program. If the remaining 90 bases were perfectly matched thefinal percent identity would be 90%. In another example, a 90 basesubject sequence is compared with a 100 base query sequence. This timethe deletions are internal deletions so that there are no bases on the5′ or 3′ of the subject sequence which are not matched/aligned with thequery. In this case the percent identity calculated by FASTDB is notmanually corrected. Once again, only bases 5′ and 3′ of the subjectsequence which are not matched/aligned with the query sequence aremanually corrected for. No other manual corrections are to made for thepurposes of the present invention.

By a polypeptide having an amino acid sequence at least, for example,95% “identical” to a query amino acid sequence of the present invention,it is intended that the amino acid sequence of the subject polypeptideis identical to the query sequence except that the subject polypeptidesequence may include up to five amino acid alterations per each 100amino acids of the query amino acid sequence. In other words, to obtaina polypeptide having an amino acid sequence at least 95% identical to aquery amino acid sequence, up to 5% of the amino acid residues in thesubject sequence may be inserted, deleted, (indels) or substituted withanother amino acid. These alterations of the reference sequence mayoccur at the amino or carboxy terminal positions of the reference aminoacid sequence or anywhere between those terminal positions, interspersedeither individually among residues in the reference sequence or in oneor more contiguous groups within the reference sequence.

As a practical matter, whether any particular polypeptide is at least90%, 95%, 96%, 97%, 98% or 99% identical to, for instance, the aminoacid sequences shown in Table 1 or to the amino acid sequence encoded bydeposited DNA clone can be determined conventionally using knowncomputer programs. A preferred method for determing the best overallmatch between a query sequence (a sequence of the present invention) anda subject sequence, also referred to as a global sequence alignment, canbe determined using the FASTDB computer program based on the algorithmof Brutlag et al. (Comp. App. Biosci. (1990) 6:237-245). In a sequencealignment the query and subject sequences are either both nucleotidesequences or both amino acid sequences. The result of said globalsequence alignment is in percent identity. Preferred parameters used ina FASTDB amino acid alignment are: Matrix=PAM 0, k-tuple=2, MismatchPenalty=1, Joining Penalty=20, Randomization Group Length=0, CutoffScore=1, Window Size=sequence length, Gap Penalty=5, Gap SizePenalty=0.05, Window Size=500 or the length of the subject amino acidsequence, whichever is shorter.

If the subject sequence is shorter than the query sequence due to N- orC-terminal deletions, not because of internal deletions, a manualcorrection must be made to the results. This is because the FASTDBprogram does not account for N- and C-terminal truncations of thesubject sequence when calculating global percent identity. For subjectsequences truncated at the N- and C-termini, relative to the the querysequence, the percent identity is corrected by calculating the number ofresidues of the query sequence that are N- and C-terminal of the subjectsequence, which are not matched/aligned with a corresponding subjectresidue, as a percent of the total bases of the query sequence. Whethera residue is matched/aligned is determined by results of the FASTDBsequence alignment. This percentage is then subtracted from the percentidentity, calculated by the above FASTDB program using the specifiedparameters, to arrive at a final percent identity score. This finalpercent identity score is what is used for the purposes of the presentinvention. Only residues to the N- and C-termini of the subjectsequence, which are not matched/aligned with the query sequence, areconsidered for the purposes of manually adjusting the percent identityscore. That is, only query residue positions outside the farthest N- andC-terminal residues of the subject sequence.

For example, a 90 amino acid residue subject sequence is aligned with a100 residue query sequence to determine percent identity. The deletionoccurs at the N-terminus of the subject sequence and therefore, theFASTDB alignment does not show a matching/alignment of the first 10residues at the N-terminus. The 10 unpaired residues represent 10% ofthe sequence (number of residues at the N- and C-termini notmatched/total number of residues in the query sequence) so 10% issubtracted from the percent identity score calculated by the FASTDBprogram. If the remaining 90 residues were perfectly matched the finalpercent identity would be 90%. In another example, a 90 residue subjectsequence is compared with a 100 residue query sequence. This time thedeletions are internal deletions so there are no residues at the N- orC-termini of the subject sequence which are not matched/aligned with thequery. In this case the percent identity calculated by FASTDB is notmanually corrected. Once again, only residue positions outside the N-and C-terminal ends of the subject sequence, as displayed in the FASTDBalignment, which are not matched/aligned with the query sequence aremanually corrected for. No other manual corrections are to made for thepurposes of the present invention.

The variants may contain alterations in the coding regions, non-codingregions, or both. Especially preferred are polynucleotide variantscontaining alterations which produce silent substitutions, additions, ordeletions, but do not alter the properties or activities of the encodedpolypeptide. Nucleotide variants produced by silent substitutions due tothe degeneracy of the genetic code are preferred. Moreover, variants inwhich 5-10, 1-5, or 1-2 amino acids are substituted, deleted, or addedin any combination are also preferred. Polynucleotide variants can beproduced for a variety of reasons, e.g., to optimize codon expressionfor a particular host (change codons in the human mRNA to thosepreferred by a bacterial host such as E. coli).

Naturally occurring variants are called “allelic variants,” and refer toone of several alternate forms of a gene occupying a given locus on achromosome of an organism. (Genes II, Lewin, B., ed., John Wiley & Sons,New York (1985).) These allelic variants can vary at either thepolynucleotide and/or polypeptide level. Alternatively, non-naturallyoccurring variants may be produced by mutagenesis techniques or bydirect synthesis.

Using known methods of protein engineering and recombinant DNAtechnology, variants may be generated to improve or alter thecharacteristics of the polypeptides of the present invention. Forinstance, one or more amino acids can be deleted from the N-terminus orC-terminus of the secreted protein without substantial loss ofbiological function. The authors of Ron et al., J. Biol. Chem. 268:2984-2988 (1993), reported variant KGF proteins having heparin bindingactivity even after deleting 3, 8, or 27 amino-terminal amino acidresidues. Similarly, Interferon gamma exhibited up to ten times higheractivity after deleting 8-10 amino acid residues from the carboxyterminus of this protein. (Dobeli et al., J. Biotechnology 7:199-216(1988).)

Moreover, ample evidence demonstrates that variants often retain abiological activity similar to that of the naturally occurring protein.For example, Gayle and coworkers (J. Biol. Chem 268:22105-22111 (1993))conducted extensive mutational analysis of human cytokine IL-la. Theyused random mutagenesis to generate over 3,500 individual IL-1a mutantsthat averaged 2.5 amino acid changes per variant over the entire lengthof the molecule. Multiple mutations were examined at every possibleamino acid position. The investigators found that “[m]ost of themolecule could be altered with little effect on either [binding orbiological activity].” (See, Abstract.) In fact, only 23 unique aminoacid sequences, out of more than 3,500 nucleotide sequences examined,produced a protein that significantly differed in activity fromwild-type.

Furthermore, even if deleting one or more amino acids from theN-terminus or C-terminus of a polypeptide results in modification orloss of one or more biological functions, other biological activitiesmay still be retained. For example, the ability of a deletion variant toinduce and/or to bind antibodies which recognize the secreted form willlikely be retained when less than the majority of the residues of thesecreted form are removed from the N-terminus or C-terminus. Whether aparticular polypeptide lacking N- or C-terminal residues of a proteinretains such immunogenic activities can readily be determined by routinemethods described herein and otherwise known in the art.

Thus, the invention further includes polypeptide variants which showsubstantial biological activity. Such variants include deletions,insertions, inversions, repeats, and substitutions selected according togeneral rules known in the art so as have little effect on activity. Forexample, guidance concerning how to make phenotypically silent aminoacid substitutions is provided in Bowie, J. U. et al., Science247:1306-1310 (1990), wherein the authors indicate that there are twomain strategies for studying the tolerance of an amino acid sequence tochange.

The first strategy exploits the tolerance of amino acid substitutions bynatural selection during the process of evolution. By comparing aminoacid sequences in different species, conserved amino acids can beidentified. These conserved amino acids are likely important for proteinfunction. In contrast, the amino acid positions where substitutions havebeen tolerated by natural selection indicates that these positions arenot critical for protein function. Thus, positions tolerating amino acidsubstitution could be modified while still maintaining biologicalactivity of the protein.

The second strategy uses genetic engineering to introduce amino acidchanges at specific positions of a cloned gene to identify regionscritical for protein function. For example, site directed mutagenesis oralanine-scanning mutagenesis (introduction of single alanine mutationsat every residue in the molecule) can be used. (Cunningham and Wells,Science 244:1081-1085 (1989).) The resulting mutant molecules can thenbe tested for biological activity.

As the authors state, these two strategies have revealed that proteinsare surprisingly tolerant of amino acid substitutions. The authorsfurther indicate which amino acid changes are likely to be permissive atcertain amino acid positions in the protein. For example, most buried(within the tertiary structure of the protein) amino acid residuesrequire nonpolar side chains, whereas few features of surface sidechains are generally conserved. Moreover, tolerated conservative aminoacid substitutions involve replacement of the aliphatic or hydrophobicamino acids Ala, Val, Leu and Ile; replacement of the hydroxyl residuesSer and Thr; replacement of the acidic residues Asp and Glu; replacementof the amide residues Asn and Gln, replacement of the basic residuesLys, Arg, and His; replacement of the aromatic residues Phe, Tyr, andTrp, and replacement of the small-sized amino acids Ala, Ser, Thr, Met,and Gly.

Besides conservative amino acid substitution, variants of the presentinvention include (i) substitutions with one or more of thenon-conserved amino acid residues, where the substituted amino acidresidues may or may not be one encoded by the genetic code, or (ii)substitution with one or more of amino acid residues having asubstituent group, or (iii) fusion of the mature polypeptide withanother compound, such as a compound to increase the stability and/orsolubility of the polypeptide (for example, polyethylene glycol), or(iv) fusion of the polypeptide with additional amino acids, such as anIgG Fc fusion region peptide, or leader or secretory sequence, or asequence facilitating purification. Such variant polypeptides are deemedto be within the scope of those skilled in the art from the teachingsherein.

For example, polypeptide variants containing amino acid substitutions ofcharged amino acids with other charged or neutral amino acids mayproduce proteins with improved characteristics, such as lessaggregation. Aggregation of pharmaceutical formulations both reducesactivity and increases clearance due to the aggregate's immunogenicactivity. (Pinckard et al., Clin. Exp. Immunol. 2:331-340 (1967);Robbins et al., Diabetes 36: 838-845 (1987); Cleland et al., Crit. Rev.Therapeutic Drug Carrier Systems 10:307-377 (1993).)

Polynucleotide and Polypeptide Fragments

In the present invention, a “polynucleotide fragment” refers to a shortpolynucleotide having a nucleic acid sequence contained in the depositedclone or shown in SEQ ID NO:X. The short nucleotide fragments arepreferably at least about 15 nt, and more preferably at least about 20nt, still more preferably at least about 30 nt, and even morepreferably, at least about 40 nt in length. A fragment “at least 20 ntin length,” for example, is intended to include 20 or more contiguousbases from the cDNA sequence contained in the deposited clone or thenucleotide sequence shown in SEQ ID NO:X. These nucleotide fragments areuseful as diagnostic probes and primers as discussed herein. Of course,larger fragments (e.g., 50, 150, 500, 600, 2000 nucleotides) arepreferred.

Moreover, representative examples of polynucleotide fragments of theinvention, include, for example, fragments having a sequence from aboutnucleotide number 1-50, 51-100, 101-150, 151-200, 201-250, 251-300,301-350, 351-400, 401-450, 451-500, 501-550, 551-600, 651-700, 701-750,751-800, 800-850, 851-900, 901-950, 951-1000, 1001-1050, 1051-1100,1101-1150, 1151-1200, 1201-1250, 1251-1300, 1301-1350, 1351-1400,1402-1450, 1451-1500, 1501-1550, 1551-1600, 1601-1650, 1651-1700,1701-1750, 1751-1800, 1801-1850, 1851-1900, 1901-1950, 1951-2000, or2001 to the end of SEQ ID NO:X or the cDNA contained in the depositedclone. In this context “about” includes the particularly recited ranges,larger or smaller by several (5, 4, 3, 2, or 1) nucleotides, at eitherterminus or at both termini. Preferably, these fragments encode apolypeptide which has biological activity. More preferably, thesepolynucleotides can be used as probes or primers as discussed herein.

In the present invention, a “polypeptide fragment” refers to a shortamino acid sequence contained in SEQ ID NO:Y or encoded by the cDNAcontained in the deposited clone. Protein fragments may be“free-standing,” or comprised within a larger polypeptide of which thefragment forms a part or region, most preferably as a single continuousregion. Representative examples of polypeptide fragments of theinvention, include, for example, fragments from about amino acid number1-20, 21-40, 41-60, 61-80, 81-100, 102-120, 121-140, 141-160, or 161 tothe end of the coding region. Moreover, polypeptide fragments can beabout 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, or 150amino acids in length. In this context “about” includes the particularlyrecited ranges, larger or smaller by several (5, 4, 3, 2, or 1) aminoacids, at either extreme or at both extremes.

Preferred polypeptide fragments include the secreted protein as well asthe mature form. Further preferred polypeptide fragments include thesecreted protein or the mature form having a continuous series ofdeleted residues from the amino or the carboxy terminus, or both. Forexample, any number of amino acids, ranging from 1-60, can be deletedfrom the amino terminus of either the secreted polypeptide or the matureform. Similarly, any number of amino acids, ranging from 1-30, can bedeleted from the carboxy terminus of the secreted protein or matureform. Furthermore, any combination of the above amino and carboxyterminus deletions are preferred. Similarly, polynucleotide fragmentsencoding these polypeptide fragments are also preferred.

Also preferred are polypeptide and polynucleotide fragmentscharacterized by structural or functional domains, such as fragmentsthat comprise alpha-helix and alpha-helix forming regions, beta-sheetand beta-sheet-forming regions, turn and turn-forming regions, coil andcoil-forming regions, hydrophilic regions, hydrophobic regions, alphaamphipathic regions, beta amphipathic regions, flexible regions,surface-forming regions, substrate binding region, and high antigenicindex regions. Polypeptide fragments of SEQ ID NO:Y falling withinconserved domains are specifically contemplated by the presentinvention. Moreover, polynucleotide fragments encoding these domains arealso contemplated.

Other preferred fragments are biologically active fragments.Biologically active fragments are those exhibiting activity similar, butnot necessarily identical, to an activity of the polypeptide of thepresent invention. The biological activity of the fragments may includean improved desired activity, or a decreased undesirable activity.

Epitopes & Antibodies

In the present invention, “epitopes” refer to polypeptide fragmentshaving antigenic or immunogenic activity in an animal, especially in ahuman. A preferred embodiment of the present invention relates to apolypeptide fragment comprising an epitope, as well as thepolynucleotide encoding this fragment. A region of a protein molecule towhich an antibody can bind is defined as an “antigenic epitope.” Incontrast, an “immunogenic epitope” is defined as a part of a proteinthat elicits an antibody response. (See, for instance, Geysen et al.,Proc. Natl. Acad. Sci. USA 81:3998-4002 (1983).)

Fragments which function as epitopes may be produced by any conventionalmeans. (See, e.g., Houghten, R. A., Proc. Natl. Acad. Sci. USA82:5131-5135 (1985) further described in U.S. Pat. No. 4,631,211.)

In the present invention, antigenic epitopes preferably contain asequence of at least seven, more preferably at least nine, and mostpreferably between about 15 to about 30 amino acids. Antigenic epitopesare useful to raise antibodies, including monoclonal antibodies, thatspecifically bind the epitope. (See, for instance, Wilson et al., Cell37:767-778 (1984); Sutcliffe, J. G. et al., Science 219:660-666 (1983).)

Similarly, immunogenic epitopes can be used to induce antibodiesaccording to methods well known in the art. (See, for instance,Sutcliffe et al., supra; Wilson et al., supra; Chow, M. et al., Proc.Natl. Acad. Sci. USA 82:910-914; and Bittle, F. J. et al., J. Gen.Virol. 66:2347-2354 (1985).) A preferred immunogenic epitope includesthe secreted protein. The immunogenic epitopes may be presented togetherwith a carrier protein, such as an albumin, to an animal system (such asrabbit or mouse) or, if it is long enough (at least about 25 aminoacids), without a carrier. However, immunogenic epitopes comprising asfew as 8 to 10 amino acids have been shown to be sufficient to raiseantibodies capable of binding to, at the very least, linear epitopes ina denatured polypeptide (e.g., in Western blotting.)

As used herein, the term “antibody” (Ab) or “monoclonal antibody” (Mab)is meant to include intact molecules as well as antibody fragments (suchas, for example, Fab and F(ab′)2 fragments) which are capable ofspecifically binding to protein. Fab and F(ab′)2 fragments lack the Fcfragment of intact antibody, clear more rapidly from the circulation,and may have less non-specific tissue binding than an intact antibody.(Wahl et al., J. Nucl. Med. 24:316-325 (1983).) Thus, these fragmentsare preferred, as well as the products of a FAB or other immunoglobulinexpression library. Moreover, antibodies of the present inventioninclude chimeric, single chain, and humanized antibodies.

Fusion Proteins

Any polypeptide of the present invention can be used to generate fusionproteins. For example, the polypeptide of the present invention, whenfused to a second protein, can be used as an antigenic tag. Antibodiesraised against the polypeptide of the present invention can be used toindirectly detect the second protein by binding to the polypeptide.Moreover, because secreted proteins target cellular locations based ontrafficking signals, the polypeptides of the present invention can beused as targeting molecules once fused to other proteins.

Examples of domains that can be fused to polypeptides of the presentinvention include not only heterologous signal sequences, but also otherheterologous functional regions. The fusion does not necessarily need tobe direct, but may occur through linker sequences.

Moreover, fusion proteins may also be engineered to improvecharacteristics of the polypeptide of the present invention. Forinstance, a region of additional amino acids, particularly charged aminoacids, may be added to the N-terminus of the polypeptide to improvestability and persistence during purification from the host cell orsubsequent handling and storage. Also, peptide moieties may be added tothe polypeptide to facilitate purification. Such regions may be removedprior to final preparation of the polypeptide. The addition of peptidemoieties to facilitate handling of polypeptides are familiar and routinetechniques in the art.

Moreover, polypeptides of the present invention, including fragments,and specifically epitopes, can be combined with parts of the constantdomain of immunoglobulins (IgG), resulting in chimeric polypeptides.These fusion proteins facilitate purification and show an increasedhalf-life in vivo. One reported example describes chimeric proteinsconsisting of the first two domains of the human CD4-polypeptide andvarious domains of the constant regions of the heavy or light chains ofmammalian immunoglobulins. (EP A 394,827; Traunecker et al., Nature331:84-86 (1988).) Fusion proteins having disulfide-linked dimericstructures (due to the IgG) can also be more efficient in binding andneutralizing other molecules, than the monomeric secreted protein orprotein fragment alone. (Fountoulakis et al., J. Biochem. 270:3958-3964(1995).)

Similarly, EP-A-O 464 533 (Canadian counterpart 2045869) disclosesfusion proteins comprising various portions of constant region ofimmunoglobulin molecules together with another human protein or partthereof. In many cases, the Fc part in a fusion protein is beneficial intherapy and diagnosis, and thus can result in, for example, improvedpharmacokinetic properties. (EP-A 0232 262.) Alternatively, deleting theFc part after the fusion protein has been expressed, detected, andpurified, would be desired. For example, the Fc portion may hindertherapy and diagnosis if the fusion protein is used as an antigen forimmunizations. In drug discovery, for example, human proteins, such ashIL-5, have been fused with Fc portions for the purpose ofhigh-throughput screening assays to identify antagonists of hIL-5. (See,D. Bennett et al., J. Molecular Recognition 8:52-58 (1995); K. Johansonet al., J. Biol. Chem. 270:9459-9471 (1995).)

Moreover, the polypeptides of the present invention can be fused tomarker sequences, such as a peptide which facilitates purification ofthe fused polypeptide. In preferred embodiments, the marker amino acidsequence is a hexa-histidine peptide, such as the tag provided in a pQEvector (QIAGEN, Inc., 9259 Eton Avenue, Chatsworth, Calif., 91311),among others, many of which are commercially available. As described inGentz et al., Proc. Natl. Acad. Sci. USA 86:821-824 (1989), forinstance, hexa-histidine provides for convenient purification of thefusion protein. Another peptide tag useful for purification, the “HA”tag, corresponds to an epitope derived from the influenza hemagglutininprotein. (Wilson et al., Cell 37:767 (1984).)

Thus, any of these above fusions can be engineered using thepolynucleotides or the polypeptides of the present invention.

Vectors, Host Cells, and Protein Production

The present invention also relates to vectors containing thepolynucleotide of the present invention, host cells, and the productionof polypeptides by recombinant techniques. The vector may be, forexample, a phage, plasmid, viral, or retroviral vector. Retroviralvectors may be replication competent or replication defective. In thelatter case, viral propagation generally will occur only incomplementing host cells.

The polynucleotides may be joined to a vector containing a selectablemarker for propagation in a host. Generally, a plasmid vector isintroduced in a precipitate, such as a calcium phosphate precipitate, orin a complex with a charged lipid. If the vector is a virus, it may bepackaged in vitro using an appropriate packaging cell line and thentransduced into host cells.

The polynucleotide insert should be operatively linked to an appropriatepromoter, such as the phage lambda PL promoter, the E. coli lac, trp,phoA and tac promoters, the SV40 early and late promoters and promotersof retroviral LTRs, to name a few. Other suitable promoters will beknown to the skilled artisan. The expression constructs will furthercontain sites for transcription initiation, termination, and, in thetranscribed region, a ribosome binding site for translation. The codingportion of the transcripts expressed by the constructs will preferablyinclude a translation initiating codon at the beginning and atermination codon (UAA, UGA or UAG) appropriately positioned at the endof the polypeptide to be translated.

As indicated, the expression vectors will preferably include at leastone selectable marker. Such markers include dihydrofolate reductase,G418 or neomycin resistance for eukaryotic cell culture andtetracycline, kanamycin or ampicillin resistance genes for culturing inE. coli and other bacteria. Representative examples of appropriate hostsinclude, but are not limited to, bacterial cells, such as E. coli,Streptomyces and Salmonella typhimurium cells; fungal cells, such asyeast cells; insect cells such as Drosophila S2 and Spodoptera Sf9cells; animal cells such as CHO, COS, 293, and Bowes melanoma cells; andplant cells. Appropriate culture mediums and conditions for theabove-described host cells are known in the art.

Among vectors preferred for use in bacteria include pQE70, pQE60 andpQE-9, available from QIAGEN, Inc.; pBluescript vectors, Phagescriptvectors, pNH8A, pNH16a, pNH18A, pNH46A, available from StratageneCloning Systems, Inc.; and ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5available from Pharmacia Biotech, Inc. Among preferred eukaryoticvectors are pWLNEO, pSV2CAT, pOG44, pXT1 and pSG available fromStratagene; and pSVK3, pBPV, pMSG and pSVL available from Pharmacia.Other suitable vectors will be readily apparent to the skilled artisan.

Introduction of the construct into the host cell can be effected bycalcium phosphate transfection, DEAE-dextran mediated transfection,cationic lipid-mediated transfection, electroporation, transduction,infection, or other methods. Such methods are described in many standardlaboratory manuals, such as Davis et al., Basic Methods In MolecularBiology (1986). It is specifically contemplated that the polypeptides ofthe present invention may in fact be expressed by a host cell lacking arecombinant vector.

A polypeptide of this invention can be recovered an d purified fromrecombinant cell cultures by well-known methods including ammoniumsulfate or ethanol precipitation, acid extraction, anion or cationexchange chromatography, phosphocellulose chromatography, hydrophobicinteraction chromatography, affinity chromatography, hydroxylapatitechromatography and lectin chromatography. Most preferably, highperformance liquid chromatography (“HPLC”) is employed for purification.

Polypeptides of the present invention, and preferably the secreted form,can also be recovered from: products purified from natural sources,including bodily fluids, tissues and cells, whether directly isolated orcultured; products of chemical synthetic procedures; and productsproduced by recombinant techniques from a prokaryotic or eukaryotichost, including, for example, bacterial, yeast, higher plant, insect,and manmmalian cells. Depending upon the host employed in a recombinantproduction procedure, the polypeptides of the present invention may beglycosylated or may be non-glycosylated. In addition, polypeptides ofthe invention may also include an initial modified methionine residue,in some cases as a result of host-mediated processes. Thus, it is wellknown in the art that the N-terminal methionine encoded by thetranslation initiation codon generally is removed with high efficiencyfrom any protein after translation in all eukaryotic cells. While theN-terminal methionine on most proteins also is efficiently removed inmost prokaryotes, for some proteins, this prokaryotic removal process isinefficient, depending on the nature of the amino acid to which theN-terminal methionine is covalently linked.

Uses of the Polynucleotides

Each of the polynucleotides identified herein can be used in numerousways as reagents. The following description should be consideredexemplary and utilizes known techniques.

The polynucleotides of the present invention are useful for chromosomeidentification. There exists an ongoing need to identify new chromosomemarkers, since few chromosome marking reagents, based on actual sequencedata (repeat polymorphisms), are presently available. Eachpolynucleotide of the present invention can be used as a chromosomemarker.

Briefly, sequences can be mapped to chromosomes by preparing PCR primers(preferably 15-25 bp) from the sequences shown in SEQ ID NO:X. Primerscan be selected using computer analysis so that primers do not span morethan one predicted exon in the genomic DNA. These primers are then usedfor PCR screening of somatic cell hybrids containing individual humanchromosomes. Only those hybrids containing the human gene correspondingto the SEQ ID NO:X will yield an amplified fragment.

Similarly, somatic hybrids provide a rapid method of PCR mapping thepolynucleotides to particular chromosomes. Three or more clones can beassigned per day using a single thermal cycler. Moreover,sublocalization of the polynucleotides can be achieved with panels ofspecific chromosome fragments. Other gene mapping strategies that can beused include in situ hybridization, prescreening with labeledflow-sorted chromosomes, and preselection by hybridization to constructchromosome specific-cDNA libraries.

Precise chromosomal location of the polynucleotides can also be achievedusing fluorescence in situ hybridization (FISH) of a metaphasechromosomal spread. This technique uses polynucleotides as short as 500or 600 bases; however, polynucleotides 2,000-4,000 bp are preferred. Fora review of this technique, see Verma et al., “Human Chromosomes: aManual of Basic Techniques,” Pergamon Press, New York (1988).

For chromosome mapping, the polynucleotides can be used individually (tomark a single chromosome or a single site on that chromosome) or inpanels (for marking multiple sites and/or multiple chromosomes).Preferred polynucleotides, correspond to the noncoding regions of thecDNAs because the coding sequences are more likely conserved within genefamilies, thus increasing the chance of cross hybridization duringchromosomal mapping.

Once a polynucleotide has been mapped to a precise chromosomal location,the physical position of the polynucleotide can be used in linkageanalysis. Linkage analysis establishes coinheritance between achromosomal location and presentation of a particular disease. (Diseasemapping data are found, for example, in V. McKusick, MendelianInheritance in Man (available on line through Johns Hopkins UniversityWelch Medical Library).) Assuming 1 megabase mapping resolution and onegene per 20 kb, a cDNA precisely localized to a chromosomal regionassociated with the disease could be one of 50-500 potential causativegenes.

Thus, once coinheritance is established, differences in thepolynucleotide and the corresponding gene between affected andunaffected individuals can be examined. First, visible structuralalterations in the chromosomes, such as deletions or translocations, areexamined in chromosome spreads or by PCR. If no structural alterationsexist, the presence of point mutations are ascertained. Mutationsobserved in some or all affected individuals, but not in normalindividuals, indicates that the mutation may cause the disease. However,complete sequencing of the polypeptide and the corresponding gene fromseveral normal individuals is required to distinguish the mutation froma polymorphism. If a new polymorphism is identified, this polymorphicpolypeptide can be used for further linkage analysis.

Furthermore, increased or decreased expression of the gene in affectedindividuals as compared to unaffected individuals can be assessed usingpolynucleotides of the present invention. Any of these alterations(altered expression, chromosomal rearrangement, or mutation) can be usedas a diagnostic or prognostic marker.

In addition to the foregoing, a polynucleotide can be used to controlgene expression through triple helix formation or antisense DNA or RNA.Both methods rely on binding of the polynucleotide to DNA or RNA. Forthese techniques, preferred polynucleotides are usually 20 to 40 basesin length and complementary to either the region of the gene involved intranscription (triple helix—see Lee et al., Nucl. Acids Res. 6:3073(1979); Cooney et al., Science 241:456 (1988); and Dervan et al.,Science 251:1360 (1991) ) or to the mRNA itself (antisense—Okano, J.Neurochem. 56:560 (1991); Oligodeoxy-nucleotides as Antisense Inhibitorsof Gene Expression, CRC Press, Boca Raton, Fla. (1988).) Triple helixformation optimally results in a shut-off of RNA transcription from DNA,while antisense RNA hybridization blocks translation of an mRNA moleculeinto polypeptide. Both techniques are effective in model systems, andthe information disclosed herein can be used to design antisense ortriple helix polynucleotides in an effort to treat disease.

Polynucleotides of the present invention are also useful in genetherapy. One goal of gene therapy is to insert a normal gene into anorganism having a defective gene, in an effort to correct the geneticdefect. The polynucleotides disclosed in the present invention offer ameans of targeting such genetic defects in a highly accurate manner.Another goal is to insert a new gene that was not present in the hostgenome, thereby producing a new trait in the host cell.

The polynucleotides are also useful for identifying individuals fromminute biological samples. The United States military, for example, isconsidering the use of restriction fragment length polymorphism (RFLP)for identification of its personnel. In this technique, an individual'sgenomic DNA is digested with one or more restriction enzymes, and probedon a Southern blot to yield unique bands for identifying personnel. Thismethod does not suffer from the current limitations of “Dog Tags” whichcan be lost, switched, or stolen, making positive identificationdifficult. The polynucleotides of the present invention can be used asadditional DNA markers for RFLP.

The polynucleotides of the present invention can also be used as analternative to RFLP, by determining the actual base-by-base DNA sequenceof selected portions of an individual's genome. These sequences can beused to prepare PCR primers for amplifying and isolating such selectedDNA, which can then be sequenced. Using this technique, individuals canbe identified because each individual will have a unique set of DNAsequences. Once an unique ID database is established for an individual,positive identification of that individual, living or dead, can be madefrom extremely small tissue samples.

Forensic biology also benefits from using DNA-based identificationtechniques as disclosed herein. DNA sequences taken from very smallbiological samples such as tissues, e.g., hair or skin, or body fluids,e.g., blood, saliva, semen, etc., can be amplified using PCR. In oneprior art technique, gene sequences amplified from polymorphic loci,such as DQa class II HLA gene, are used in forensic biology to identifyindividuals. (Erlich, H., PCR Technology, Freeman and Co. (1992).) Oncethese specific polymorphic loci are amplified, they are digested withone or more restriction enzymes, yielding an identifying set of bands ona Southern blot probed with DNA corresponding to the DQa class II HLAgene. Similarly, polynucleotides of the present invention can be used aspolymorphic markers for forensic purposes.

There is also a need for reagents capable of identifying the source of aparticular tissue. Such need arises, for example, in forensics whenpresented with tissue of unknown origin. Appropriate reagents cancomprise, for example, DNA probes or primers specific to particulartissue prepared from the sequences of the present invention. Panels ofsuch reagents can identify tissue by species and/or by organ type. In asimilar fashion, these reagents can be used to screen tissue culturesfor contamination.

In the very least, the polynucleotides of the present invention can beused as molecular weight markers on Southern gels, as diagnostic probesfor the presence of a specific mRNA in a particular cell type, as aprobe to “subtract-out” known sequences in the process of discoveringnovel polynucleotides, for selecting and making oligomers for attachmentto a “gene chip” or other support, to raise anti-DNA antibodies usingDNA immunization techniques, and as an antigen to elicit an immuneresponse.

Uses of the Polypeptides

Each of the polypeptides identified herein can be used in numerous ways.The following description should be considered exemplary and utilizesknown techniques.

A polypeptide of the present invention can be used to assay proteinlevels in a biological sample using antibody-based techniques. Forexample, protein expression in tissues can be studied with classicalimmunohistological methods. (Jalkanen, M., et al., J. Cell. Biol.101:976-985 (1985); Jalkanen, M., et al., J. Cell. Biol. 105:3087-3096(1987).) Other antibody-based methods useful for detecting protein geneexpression include immunoassays, such as the enzyme linked immunosorbentassay (ELISA) and the radioimmunoassay (RIA). Suitable antibody assaylabels are known in the art and include enzyme labels, such as, glucoseoxidase, and radioisotopes, such as iodine (125I, 121I), carbon (14C),sulfur (35S), tritium (3H), indium (112In), and technetium (99mTc), andfluorescent labels, such as fluorescein and rhodamine, and biotin.

In addition to assaying secreted protein levels in a biological sample,proteins can also be detected in vivo by imaging. Antibody labels ormarkers for in vivo imaging of protein include those detectable byX-radiography, NMR or ESR. For X-radiography, suitable labels includeradioisotopes such as barium or cesium, which emit detectable radiationbut are not overtly harmful to the subject. Suitable markers for NMR andESR include those with a detectable characteristic spin, such asdeuterium, which may be incorporated into the antibody by labeling ofnutrients for the relevant hybridoma.

A protein-specific antibody or antibody fragment which has been labeledwith an appropriate detectable imaging moiety, such as a radioisotope(for example, 131I, 112In, 99mTc), a radio-opaque substance, or amaterial detectable by nuclear magnetic resonance, is introduced (forexample, parenterally, subcutaneously, or intraperitoneally) into themammal. It will be understood in the art that the size of the subjectand the imaging system used will determine the quantity of imagingmoiety needed to produce diagnostic images. In the case of aradioisotope moiety, for a human subject, the quantity of radioactivityinjected will normally range from about 5 to 20 millicuries of 99mTc.The labeled antibody or antibody fragment will then preferentiallyaccumulate at the location of cells which contain the specific protein.In vivo tumor imaging is described in S. W. Burchiel et al.,“Immunopharmacokinetics of Radiolabeled Antibodies and Their Fragments.”(Chapter 13 in Tumor Imaging: The Radiochemical Detection of Cancer, S.W. Burchiel and B. A. Rhodes, eds., Masson Publishing Inc. (1982).)

Thus, the invention provides a diagnostic method of a disorder, whichinvolves (a) assaying the expression of a polypeptide of the presentinvention in cells or body fluid of an individual; (b) comparing thelevel of gene expression with a standard gene expression level, wherebyan increase or decrease in the assayed polypeptide gene expression levelcompared to the standard expression level is indicative of a disorder.

Moreover, polypeptides of the present invention can be used to treatdisease. For example, patients can be administered a polypeptide of thepresent invention in an effort to replace absent or decreased levels ofthe polypeptide (e.g., insulin), to supplement absent or decreasedlevels of a different polypeptide (e.g., hemoglobin S for hemoglobin B),to inhibit the activity of a polypeptide (e.g., an oncogene), toactivate the activity of a polypeptide (e.g., by binding to a receptor),to reduce the activity of a membrane bound receptor by competing with itfor free ligand (e.g., soluble TNF receptors used in reducinginflammation), or to bring about a desired response (e.g., blood vesselgrowth).

Similarly, antibodies directed to a polypeptide of the present inventioncan also be used to treat disease. For example, administration of anantibody directed to a polypeptide of the present invention can bind andreduce overproduction of the polypeptide. Similarly, administration ofan antibody can activate the polypeptide, such as by binding to apolypeptide bound to a membrane (receptor).

At the very least, the polypeptides of the present invention can be usedas molecular weight markers on SDS-PAGE gels or on molecular sieve gelfiltration columns using methods well known to those of skill in theart. Polypeptides can also be used to raise antibodies, which in turnare used to measure protein expression from a recombinant cell, as a wayof assessing transformation of the host cell. Moreover, the polypeptidesof the present invention can be used to test the following biologicalactivities.

Biological Activities

The polynucleotides and polypeptides of the present invention can beused in assays to test for one or more biological activities. If thesepolynucleotides and polypeptides do exhibit activity in a particularassay, it is likely that these molecules may be involved in the diseasesassociated with the biological activity. Thus, the polynucleotides andpolypeptides could be used to treat the associated disease.

Immune Activity

A polypeptide or polynucleotide of the present invention may be usefulin treating deficiencies or disorders of the immune system, byactivating or inhibiting the proliferation, differentiation, ormobilization (chemotaxis) of immune cells. Immune cells develop througha process called hematopoiesis, producing myeloid (platelets, red bloodcells, neutrophils, and macrophages) and lymphoid (B and T lymphocytes)cells from pluripotent stem cells. The etiology of these immunedeficiencies or disorders may be genetic, somatic, such as cancer orsome autoimmune disorders, acquired (e.g., by chemotherapy or toxins),or infectious. Moreover, a polynucleotide or polypeptide of the presentinvention can be used as a marker or detector of a particular immunesystem disease or disorder.

A polynucleotide or polypeptide of the present invention may be usefulin treating or detecting deficiencies or disorders of hematopoieticcells. A polypeptide or polynucleotide of the present invention could beused to increase differentiation and proliferation of hematopoieticcells, including the pluripotent stem cells, in an effort to treat thosedisorders associated with a decrease in certain (or many) typeshematopoietic cells. Examples of immunologic deficiency syndromesinclude, but are not limited to: blood protein disorders (e.g.agammaglobulinemia, dysgammaglobulinemia), ataxia telangiectasia, commonvariable immunodeficiency, Digeorge Syndrome, HIV infection, HTLV-BLVinfection, leukocyte adhesion deficiency syndrome, lymphopenia,phagocyte bactericidal dysfunction, severe combined immunodeficiency(SCIDs), Wiskott-Aldrich Disorder, anemia, thrombocytopenia, orhemoglobinuria.

Moreover, a polypeptide or polynucleotide of the present invention couldalso be used to modulate hemostatic (the stopping of bleeding) orthrombolytic activity (clot formation). For example, by increasinghemostatic or thrombolytic activity, a polynucleotide or polypeptide ofthe present invention could be used to treat blood coagulation disorders(e.g., afibrinogenemia, factor deficiencies), blood platelet disorders(e.g. thrombocytopenia), or wounds resulting from trauma, surgery, orother causes. Alternatively, a polynucleotide or polypeptide of thepresent invention that can decrease hemostatic or thrombolytic activitycould be used to inhibit or dissolve clotting. These molecules could beimportant in the treatment of heart attacks (infarction), strokes, orscarring.

A polynucleotide or polypeptide of the present invention may also beuseful in treating or detecting autoimmune disorders. Many autoimmunedisorders result from inappropriate recognition of self as foreignmaterial by immune cells. This inappropriate recognition results in animmune response leading to the destruction of the host tissue.Therefore, the administration of a polypeptide or polynucleotide of thepresent invention that inhibits an immune response, particularly theproliferation, differentiation, or chemotaxis of T-cells, may be aneffective therapy in preventing autoimmune disorders.

Examples of autoimmune disorders that can be treated or detected by thepresent invention include, but are not limited to: Addison's Disease,hemolytic anemia, antiphospholipid syndrome, rheumatoid arthritis,dermatitis, allergic encephalomyelitis, glomerulonephritis,Goodpasture's Syndrome, Graves' Disease, Multiple Sclerosis, MyastheniaGravis, Neuritis, Ophthalmia, Bullous Pemphigoid, Pemphigus,Polyendocrinopathies, Purpura, Reiter's Disease, Stiff-Man Syndrome,Autoimmune Thyroiditis, Systemic Lupus Erythematosus, AutoimmunePulmonary Inflammation, Guillain-Barre Syndrome, insulin dependentdiabetes mellitis, and autoimmune inflammatory eye disease.

Similarly, allergic reactions and conditions, such as asthma(particularly allergic asthma) or other respiratory problems, may alsobe treated by a polypeptide or polynucleotide of the present invention.Moreover, these molecules can be used to treat anaphylaxis,hypersensitivity to an antigenic molecule, or blood groupincompatibility.

A polynucleotide or polypeptide of the present invention may also beused to treat and/or prevent organ rejection or graft-versus-hostdisease (GVHD). Organ rejection occurs by host immune cell destructionof the transplanted tissue through an immune response. Similarly, animmune response is also involved in GVHD, but, in this case, the foreigntransplanted immune cells destroy the host tissues. The administrationof a polypeptide or polynucleotide of the present invention thatinhibits an immune response, particularly the proliferation,differentiation, or chemotaxis of T-cells, may be an effective therapyin preventing organ rejection or GVHD.

Similarly, a polypeptide or polynucleotide of the present invention mayalso be used to modulate inflammation. For example, the polypeptide orpolynucleotide may inhibit the proliferation and differentiation ofcells involved in an inflammatory response. These molecules can be usedto treat inflammatory conditions, both chronic and acute conditions,including inflammation associated with infection (e.g., septic shock,sepsis, or systemic inflammatory response syndrome (SIRS)),ischemia-reperfusion injury, endotoxin lethality, arthritis,complement-mediated hyperacute rejection, nephritis, cytokine orchemokine induced lung injury, inflammatory bowel disease, Crohn'sdisease, or resulting from over production of cytokines (e.g., TNF orIL-1.)

Hyperproliferative Disorders

A polypeptide or polynucleotide can be used to treat or detecthyperproliferative disorders, including neoplasms. A polypeptide orpolynucleotide of the present invention may inhibit the proliferation ofthe disorder through direct or indirect interactions. Alternatively, apolypeptide or polynucleotide of the present invention may proliferateother cells which can inhibit the hyperproliferative disorder.

For example, by increasing an immune response, particularly increasingantigenic qualities of the hyperproliferative disorder or byproliferating, differentiating, or mobilizing T-cells,hyperproliferative disorders can be treated. This immune response may beincreased by either enhancing an existing immune response, or byinitiating a new immune response. Alternatively, decreasing an immuneresponse may also be a method of treating hyperproliferative disorders,such as a chemotherapeutic agent.

Examples of hyperproliferative disorders that can be treated or detectedby a polynucleotide or polypeptide of the present invention include, butare not limited to neoplasms located in the: abdomen, bone, breast,digestive system, liver, pancreas, peritoneum, endocrine glands(adrenal, parathyroid, pituitary, testicles, ovary, thymus, thyroid),eye, head and neck, nervous (central and peripheral), lymphatic system,pelvic, skin, soft tissue, spleen, thoracic, and urogenital.

Similarly, other hyperproliferative disorders can also be treated ordetected by a polynucleotide or polypeptide of the present invention.Examples of such hyperproliferative disorders include, but are notlimited to: hypergammaglobulinemia, lymphoproliferative disorders,paraproteinemias, purpura, sarcoidosis, Sezary Syndrome, Waldenstron'sMacroglobulinemia, Gaucher's Disease, histiocytosis, and any otherhyperproliferative disease, besides neoplasia, located in an organsystem listed above.

Infectious Disease

A polypeptide or polynucleotide of the present invention can be used totreat or detect infectious agents. For example, by increasing the immuneresponse, particularly increasing the proliferation and differentiationof B and/or T cells, infectious diseases may be treated. The immuneresponse may be increased by either enhancing an existing immuneresponse, or by initiating a new immune response. Alternatively, thepolypeptide or polynucleotide of the present invention may also directlyinhibit the infectious agent, without necessarily eliciting an immuneresponse.

Viruses are one example of an infectious agent that can cause disease orsymptoms that can be treated or detected by a polynucleotide orpolypeptide of the present invention. Examples of viruses, include, butare not limited to the following DNA and RNA viral families: Arbovirus,Adenoviridae, Arenaviridae, Arterivirus, Birnaviridae, Bunyaviridae,Caliciviridae, Circoviridae, Coronaviridae, Flaviviridae, Hepadnaviridae(Hepatitis), Herpesviridae (such as, Cytomegalovirus, Herpes Simplex,Herpes Zoster), Mononegavirus (e.g., Paramyxoviridae, Morbillivirus,Rhabdoviridae), Orthomyxoviridae (e.g., Influenza), Papovaviridae,Parvoviridae, Picomaviridae, Poxviridae (such as Smallpox or Vaccinia),Reoviridae (e.g., Rotavirus), Retroviridae (HTLV-I, HTLV-II,Lentivirus), and Togaviridae (e.g., Rubivirus). Viruses falling withinthese families can cause a variety of diseases or symptoms, including,but not limited to: arthritis, bronchiollitis, encephalitis, eyeinfections (e.g., conjunctivitis, keratitis), chronic fatigue syndrome,hepatitis (A, B, C, E, Chronic Active, Delta), meningitis, opportunisticinfections (e.g., AIDS), pneumonia, Burkitt's Lymphoma, chickenpox,hemorrhagic fever, Measles, Mumps, Parainfluenza, Rabies, the commoncold, Polio, leukemia, Rubella, sexually transmitted diseases, skindiseases (e.g., Kaposi's, warts), and viremia. A polypeptide orpolynucleotide of the present invention can be used to treat or detectany of these symptoms or diseases.

Similarly, bacterial or fimgal agents that can cause disease or symptomsand that can be treated or detected by a polynucleotide or polypeptideof the present invention include, but not limited to, the followingGram-Negative and Gram-positive bacterial families and fungi:Actinomycetales (e.g., Corynebacterium, Mycobacterium, Norcardia),Aspergillosis, Bacillaceae (e.g., Anthrax, Clostridium), Bacteroidaceae,Blastomycosis, Bordetella, Borrelia, Brucellosis, Candidiasis,Campylobacter, Coccidioidomycosis, Cryptococcosis, Dermatocycoses,Enterobacteriaceae (Klebsiella, Salmonella, Serratia, Yersinia),Erysipelothrix, Helicobacter, Legionellosis, Leptospirosis, Listeria,Mycoplasmatales, Neisseriaceae (e.g., Acinetobacter, Gonorrhea,Menigococcal), Pasteurellacea Infections (e.g., Actinobacillus,Heamophilus, Pasteurella), Pseudomonas, Rickettsiaceae, Chlamydiaceae,Syphilis, and Staphylococcal. These bacterial or fIugal families cancause the following diseases or symptoms, including, but not limited to:bacteremia, endocarditis, eye infections (conjunctivitis, tuberculosis,uveitis), gingivitis, opportunistic infections (e.g., AIDS relatedinfections), paronychia, prosthesis-related infections, Reiter'sDisease, respiratory tract infections, such as Whooping Cough orEmpyema, sepsis, Lyme Disease, Cat-Scratch Disease, Dysentery,Paratyphoid Fever, food poisoning, Typhoid, pneumonia, Gonorrhea,meningitis, Chlamydia, Syphilis, Diphtheria, Leprosy, Paratuberculosis,Tuberculosis, Lupus, Botulism, gangrene, tetanus, impetigo, RheumaticFever, Scarlet Fever, sexually transmitted diseases, skin diseases(e.g., cellulitis, dermatocycoses), toxemia, urinary tract infections,wound infections. A polypeptide or polynucleotide of the presentinvention can be used to treat or detect any of these symptoms ordiseases.

Moreover, parasitic agents causing disease or symptoms that can betreated or detected by a polynucleotide or polypeptide of the presentinvention include, but not limited to, the following families:Amebiasis, Babesiosis, Coccidiosis, Cryptosporidiosis, Dientamoebiasis,Dourine, Ectoparasitic, Giardiasis, Helminthiasis, Leishmaniasis,Theileriasis, Toxoplasmosis, Trypanosomiasis, and Trichomonas. Theseparasites can cause a variety of diseases or symptoms, including, butnot limited to: Scabies, Trombiculiasis, eye infections, intestinaldisease (e.g., dysentery, giardiasis), liver disease, lung disease,opportunistic infections (e.g., AIDS related), Malaria, pregnancycomplications, and toxoplasmosis. A polypeptide or polynucleotide of thepresent invention can be used to treat or detect any of these symptomsor diseases.

Preferably, treatment using a polypeptide or polynucleotide of thepresent invention could either be by administering an effective amountof a polypeptide to the patient, or by removing cells from the patient,supplying the cells with a polynucleotide of the present invention, andreturning the engineered cells to the patient (ex vivo therapy).Moreover, the polypeptide or polynucleotide of the present invention canbe used as an antigen in a vaccine to raise an immune response againstinfectious disease.

Regeneration

A polynucleotide or polypeptide of the present invention can be used todifferentiate, proliferate, and attract cells, leading to theregeneration of tissues. (See, Science 276:59-87 (1997).) Theregeneration of tissues could be used to repair, replace, or protecttissue damaged by congenital defects, trauma (wounds, burns, incisions,or ulcers), age, disease (e.g. osteoporosis, osteocarthritis,periodontal disease, liver failure), surgery, including cosmetic plasticsurgery, fibrosis, reperfusion injury, or systemic cytokine damage.

Tissues that could be regenerated using the present invention includeorgans (e.g., pancreas, liver, intestine, kidney, skin, endothelium),muscle (smooth, skeletal or cardiac), vascular (including vascularendothelium), nervous, hematopoietic, and skeletal (bone, cartilage,tendon, and ligament) tissue. Preferably, regeneration occurs without ordecreased scarring. Regeneration also may include angiogenesis.

Moreover, a polynucleotide or polypeptide of the present invention mayincrease regeneration of tissues difficult to heal. For example,increased tendon/ligament regeneration would quicken recovery time afterdamage. A polynucleotide or polypeptide of the present invention couldalso be used prophylactically in an effort to avoid damage. Specificdiseases that could be treated include of tendinitis, carpal tunnelsyndrome, and other tendon or ligament defects. A further example oftissue regeneration of non-healing wounds includes pressure ulcers,ulcers associated with vascular insufficiency, surgical, and traumaticwounds.

Similarly, nerve and brain tissue could also be regenerated by using apolynucleotide or polypeptide of the present invention to proliferateand differentiate nerve cells. Diseases that could be treated using thismethod include central and peripheral nervous system diseases,neuropathies, or mechanical and traumatic disorders (e.g., spinal corddisorders, head trauma, cerebrovascular disease, and stoke).Specifically, diseases associated with peripheral nerve injuries,peripheral neuropathy (e.g., resulting from chemotherapy or othermedical therapies), localized neuropathies, and central nervous systemdiseases (e.g., Alzheimer's disease, Parkinson's disease, Huntington'sdisease, amyotrophic lateral sclerosis, and Shy-Drager syndrome), couldall be treated using the polynucleotide or polypeptide of the presentinvention.

Chemotaxis

A polynucleotide or polypeptide of the present invention may havechemotaxis activity. A chemotaxic molecule attracts or mobilizes cells(e.g., monocytes, fibroblasts, neutrophils, T-cells, mast cells,eosinophils, epithelial and/or endothelial cells) to a particular sitein the body, such as inflammation, infection, or site ofhyperproliferation. The mobilized cells can then fight off and/or healthe particular trauma or abnormality.

A polynucleotide or polypeptide of the present invention may increasechemotaxic activity of particular cells. These chemotactic molecules canthen be used to treat inflammation, infection, hyperproliferativedisorders, or any immune system disorder by increasing the number ofcells targeted to a particular location in the body. For example,chemotaxic molecules can be used to treat wounds and other trauma totissues by attracting immune cells to the injured location. Chemotacticmolecules of the present invention can also attract fibroblasts, whichcan be used to treat wounds.

It is also contemplated that a polynucleotide or polypeptide of thepresent invention may inhibit chemotactic activity. These moleculescould also be used to treat disorders. Thus, a polynucleotide orpolypeptide of the present invention could be used as an inhibitor ofchemotaxis.

Binding Activity

A polypeptide of the present invention may be used to screen formolecules that bind to the polypeptide or for molecules to which thepolypeptide binds. The binding of the polypeptide and the molecule mayactivate (agonist), increase, inhibit (antagonist), or decrease activityof the polypeptide or the molecule bound. Examples of such moleculesinclude antibodies, oligonucleotides, proteins (e.g., receptors),orsmall molecules.

Preferably, the molecule is closely related to the natural ligand of thepolypeptide, e.g., a fragment of the ligand, or a natural substrate, aligand, a structural or functional mimetic. (See, Coligan et al.,Current Protocols in Immunology 1(2):Chapter 5 (1991).) Similarly, themolecule can be closely related to the natural receptor to which thepolypeptide binds, or at least, a fragment of the receptor capable ofbeing bound by the polypeptide (e.g., active site). In either case, themolecule can be rationally designed using known techniques.

Preferably, the screening for these molecules involves producingappropriate cells which express the polypeptide, either as a secretedprotein or on the cell membrane. Preferred cells include cells frommammals, yeast, Drosophila, or E. coli. Cells expressing the polypeptide(or cell membrane containing the expressed polypeptide) are thenpreferably contacted with a test compound potentially containing themolecule to observe binding, stimulation, or inhibition of activity ofeither the polypeptide or the molecule.

The assay may simply test binding of a candidate compound to thepolypeptide, wherein binding is detected by a label, or in an assayinvolving competition with a labeled competitor. Further, the assay maytest whether the candidate compound results in a signal generated bybinding to the polypeptide.

Alternatively, the assay can be carried out using cell-freepreparations, polypeptide/molecule affixed to a solid support, chemicallibraries, or natural product mixtures. The assay may also simplycomprise the steps of mixing a candidate compound with a solutioncontaining a polypeptide, measuring polypeptide/molecule activity orbinding, and comparing the polypeptide/molecule activity or binding to astandard.

Preferably, an ELISA assay can measure polypeptide level or activity ina sample (e.g., biological sample) using a monoclonal or polyclonalantibody. The antibody can measure polypeptide level or activity byeither binding, directly or indirectly, to the polypeptide or bycompeting with the polypeptide for a substrate.

All of these above assays can be used as diagnostic or prognosticmarkers. The molecules discovered using these assays can be used totreat disease or to bring about a particular result in a patient (e.g.,blood vessel growth) by activating or inhibiting thepolypeptide/molecule. Moreover, the assays can discover agents which mayinhibit or enhance the production of the polypeptide from suitablymanipulated cells or tissues.

Therefore, the invention includes a method of identifying compoundswhich bind to a polypeptide of the invention comprising the steps of:(a) incubating a candidate binding compound with a polypeptide of theinvention; and (b) determining if binding has occurred. Moreover, theinvention includes a method of identifying agonists/antagonistscomprising the steps of: (a) incubating a candidate compound with apolypeptide of the invention, (b) assaying a biological activity, and(b) determining if a biological activity of the polypeptide has beenaltered.

Other Activities

A polypeptide or polynucleotide of the present invention may alsoincrease or decrease the differentiation or proliferation of embryonicstem cells, besides, as discussed above, hematopoietic lineage.

A polypeptide or polynucleotide of the present invention may also beused to modulate mammalian characteristics, such as body height, weight,hair color, eye color, skin, percentage of adipose tissue, pigmentation,size, and shape (e.g., cosmetic surgery). Similarly, a polypeptide orpolynucleotide of the present invention may be used to modulatemammalian metabolism affecting catabolism, anabolism, processing,utilization, and storage of energy.

A polypeptide or polynucleotide of the present invention may be used tochange a mammal's mental state or physical state by influencingbiorhythms, caricadic rhythms, depression (including depressivedisorders), tendency for violence, tolerance for pain, reproductivecapabilities (preferably by Activin or Inhibin-like activity), hormonalor endocrine levels, appetite, libido, memory, stress, or othercognitive qualities.

A polypeptide or polynucleotide of the present invention may also beused as a food additive or preservative, such as to increase or decreasestorage capabilities, fat content, lipid, protein, carbohydrate,vitamins, minerals, cofactors or other nutritional components.

Other Preferred Embodiments

Other preferred embodiments of the claimed invention include an isolatednucleic acid molecule comprising a nucleotide sequence which is at least95% identical to a sequence of at least about 50 contiguous nucleotidesin the nucleotide sequence of SEQ ID NO:X wherein X is any integer asdefined in Table 1.

Also preferred is a nucleic acid molecule wherein said sequence ofcontiguous nucleotides is included in the nucleotide sequence of SEQ IDNO:X in the range of positions beginning with the nucleotide at aboutthe position of the 5′ Nucleotide of the Clone Sequence and ending withthe nucleotide at about the position of the 3′ Nucleotide of the CloneSequence as defined for SEQ ID NO:X in Table 1.

Also preferred is a nucleic acid molecule wherein said sequence ofcontiguous nucleotides is included in the nucleotide sequence of SEQ IDNO:X in the range of positions beginning with the nucleotide at aboutthe position of the 5′ Nucleotide of the Start Codon and ending with thenucleotide at about the position of the 3′ Nucleotide of the CloneSequence as defined for SEQ ID NO:X in Table 1.

Similarly preferred is a nucleic acid molecule wherein said sequence ofcontiguous nucleotides is included in the nucleotide sequence of SEQ IDNO:X in the range of positions beginning with the nucleotide at aboutthe position of the 5′ Nucleotide of the First Amino Acid of the SignalPeptide and ending with the nucleotide at about the position of the 3′Nucleotide of the Clone Sequence as defined for SEQ ID NO:X in Table 1.

Also preferred is an isolated nucleic acid molecule comprising anucleotide sequence which is at least 95% identical to a sequence of atleast about 150 contiguous nucleotides in the nucleotide sequence of SEQID NO:X.

Further preferred is an isolated nucleic acid molecule comprising anucleotide sequence which is at least 95% identical to a sequence of atleast about 500 contiguous nucleotides in the nucleotide sequence of SEQID NO:X.

A further preferred embodiment is a nucleic acid molecule comprising anucleotide sequence which is at least 95% identical to the nucleotidesequence of SEQ ID NO:X beginning with the nucleotide at about theposition of the 5′ Nucleotide of the First Amino Acid of the SignalPeptide and ending with the nucleotide at about the position of the 3′Nucleotide of the Clone Sequence as defined for SEQ ID NO:X in Table 1.

A further preferred embodiment is an isolated nucleic acid moleculecomprising a nucleotide sequence which is at least 95% identical to thecomplete nucleotide sequence of SEQ ID NO:X.

Also preferred is an isolated nucleic acid molecule which hybridizesunder stringent hybridization conditions to a nucleic acid molecule,wherein said nucleic acid molecule which hybridizes does not hybridizeunder stringent hybridization conditions to a nucleic acid moleculehaving a nucleotide sequence consisting of only A residues or of only Tresidues.

Also preferred is a composition of matter comprising a DNA moleculewhich comprises a human cDNA clone identified by a cDNA Clone Identifierin Table 1, which DNA molecule is contained in the material depositedwith the American Type Culture Collection and given the ATCC DepositNumber shown in Table 1 for said cDNA Clone Identifier.

Also preferred is an isolated nucleic acid molecule comprising anucleotide sequence which is at least 95% identical to a sequence of atleast 50 contiguous nucleotides in the nucleotide sequence of a humancDNA clone identified by a cDNA Clone Identifier in Table 1, which DNAmolecule is contained in the deposit given the ATCC Deposit Number shownin Table 1.

Also preferred is an isolated nucleic acid molecule, wherein saidsequence of at least 50 contiguous nucleotides is included in thenucleotide sequence of the complete open reading frame sequence encodedby said human cDNA clone.

Also preferred is an isolated nucleic acid molecule comprising anucleotide sequence which is at least 95% identical to sequence of atleast 150 contiguous nucleotides in the nucleotide sequence encoded bysaid human cDNA clone.

A further preferred embodiment is an isolated nucleic acid moleculecomprising a nucleotide sequence which is at least 95% identical tosequence of at least 500 contiguous nucleotides in the nucleotidesequence encoded by said human cDNA clone.

A further preferred embodiment is an isolated nucleic acid moleculecomprising a nucleotide sequence which is at least 95% identical to thecomplete nucleotide sequence encoded by said human cDNA clone.

A further preferred embodiment is a method for detecting in a biologicalsample a nucleic acid molecule comprising a nucleotide sequence which isat least 95% identical to a sequence of at least 50 contiguousnucleotides in a sequence selected from the group consisting of: anucleotide sequence of SEQ ID NO:X wherein X is any integer as definedin Table 1; and a nucleotide sequence encoded by a human cDNA cloneidentified by a cDNA Clone Identifier in Table 1 and contained in thedeposit with the ATCC Deposit Number shown for said cDNA clone in Table1; which method comprises a step of comparing a nucleotide sequence ofat least one nucleic acid molecule in said sample with a sequenceselected from said group and determining whether the sequence of saidnucleic acid molecule in said sample is at least 95% identical to saidselected sequence.

Also preferred is the above method wherein said step of comparingsequences comprises determining the extent of nucleic acid hybridizationbetween nucleic acid molecules in said sample and a nucleic acidmolecule comprising said sequence selected from said group. Similarly,also preferred is the above method wherein said step of comparingsequences is performed by comparing the nucleotide sequence determinedfrom a nucleic acid molecule in said sample with said sequence selectedfrom said group. The nucleic acid molecules can comprise DNA moleculesor RNA molecules.

A further preferred embodiment is a method for identifying the species,tissue or cell type of a biological sample which method comprises a stepof detecting nucleic acid molecules in said sample, if any, comprising anucleotide sequence that is at least 95% identical to a sequence of atleast 50 contiguous nucleotides in a sequence selected from the groupconsisting of: a nucleotide sequence of SEQ ID NO:X wherein X is anyinteger as defined in Table 1; and a nucleotide sequence encoded by ahuman cDNA clone identified by a cDNA Clone Identifier in Table 1 andcontained in the deposit with the ATCC Deposit Number shown for saidcDNA clone in Table 1.

The method for identifying the species, tissue or cell type of abiological sample can comprise a step of detecting nucleic acidmolecules comprising a nucleotide sequence in a panel of at least twonucleotide sequences, wherein at least one sequence in said panel is atleast 95% identical to a sequence of at least 50 contiguous nucleotidesin a sequence selected from said group.

Also preferred is a method for diagnosing in a subject a pathologicalcondition associated with abnormal structure or expression of a geneencoding a secreted protein identified in Table 1, which methodcomprises a step of detecting in a biological sample obtained from saidsubject nucleic acid molecules, if any, comprising a nucleotide sequencethat is at least 95% identical to a sequence of at least 50 contiguousnucleotides in a sequence selected from the group consisting of: anucleotide sequence of SEQ ID NO:X wherein X is any integer as definedin Table 1; and a nucleotide sequence encoded by a human cDNA cloneidentified by a cDNA Clone Identifier in Table 1 and contained in thedeposit with the ATCC Deposit Number shown for said cDNA clone in Table1.

The method for diagnosing a pathological condition can comprise a stepof detecting nucleic acid molecules comprising a nucleotide sequence ina panel of at least two nucleotide sequences, wherein at least onesequence in said panel is at least 95% identical to a sequence of atleast 50 contiguous nucleotides in a sequence selected from said group.

Also preferred is a composition of matter comprising isolated nucleicacid molecules wherein the nucleotide sequences of said nucleic acidmolecules comprise a panel of at least two nucleotide sequences, whereinat least one sequence in said panel is at least 95% identical to asequence of at least 50 contiguous nucleotides in a sequence selectedfrom the group consisting of: a nucleotide sequence of SEQ ID NO:Xwherein X is any integer as defined in Table 1; and a nucleotidesequence encoded by a human cDNA clone identified by a cDNA CloneIdentifier in Table 1 and contained in the deposit with the ATCC DepositNumber shown for said cDNA clone in Table 1. The nucleic acid moleculescan comprise DNA molecules or RNA molecules.

Also preferred is an isolated polypeptide comprising an amino acidsequence at least 90% identical to a sequence of at least about 10contiguous amino acids in the amino acid sequence of SEQ ID NO:Y whereinY is any integer as defined in Table 1.

Also preferred is a polypeptide, wherein said sequence of contiguousamino acids is included in the amino acid sequence of SEQ ID NO:Y in therange of positions beginning with the residue at about the position ofthe First Amino Acid of the Secreted Portion and ending with the residueat about the Last Amino Acid of the Open Reading Frame as set forth forSEQ ID NO:Y in Table 1.

Also preferred is an isolated polypeptide comprising an amino acidsequence at least 95% identical to a sequence of at least about 30contiguous amino acids in the amino acid sequence of SEQ ID NO:Y.

Further preferred is an isolated polypeptide comprising an amino acidsequence at least 95% identical to a sequence of at least about 100contiguous amino acids in the amino acid sequence of SEQ ID NO:Y.

Further preferred is an isolated polypeptide comprising an amino acidsequence at least 95% identical to the complete amino acid sequence ofSEQ ID NO:Y.

Further preferred is an isolated polypeptide comprising an amino acidsequence at least 90% identical to a sequence of at least about 10contiguous amino acids in the complete amino acid sequence of a secretedprotein encoded by a human cDNA clone identified by a cDNA CloneIdentifier in Table 1 and contained in the deposit with the ATCC DepositNumber shown for said cDNA clone in Table 1.

Also preferred is a polypeptide wherein said sequence of contiguousamino acids is included in the amino acid sequence of a secreted portionof the secreted protein encoded by a human cDNA clone identified by acDNA Clone Identifier in Table 1 and contained in the deposit with theATCC Deposit Number shown for said cDNA clone in Table 1.

Also preferred is an isolated polypeptide comprising an amino acidsequence at least 95% identical to a sequence of at least about 30contiguous amino acids in the amino acid sequence of the secretedportion of the protein encoded by a human cDNA clone identified by acDNA Clone Identifier in Table 1 and contained in the deposit with theATCC Deposit Number shown for said cDNA clone in Table 1.

Also preferred is an isolated polypeptide comprising an amino acidsequence at least 95% identical to a sequence of at least about 100contiguous amino acids in the amino acid sequence of the secretedportion of the protein encoded by a human cDNA clone identified by acDNA Clone Identifier in Table 1 and contained in the deposit with theATCC Deposit Number shown for said cDNA clone in Table 1.

Also preferred is an isolated polypeptide comprising an amino acidsequence at least 95% identical to the amino acid sequence of thesecreted portion of the protein encoded by a human cDNA clone identifiedby a cDNA Clone Identifier in Table 1 and contained in the deposit withthe ATCC Deposit Number shown for said cDNA clone in Table 1.

Further preferred is an isolated antibody which binds specifically to apolypeptide comprising an amino acid sequence that is at least 90%identical to a sequence of at least 10 contiguous amino acids in asequence selected from the group consisting of: an amino acid sequenceof SEQ ID NO:Y wherein Y is any integer as defined in Table 1; and acomplete amino acid sequence of a protein encoded by a human cDNA cloneidentified by a cDNA Clone Identifier in Table 1 and contained in thedeposit with the ATCC Deposit Number shown for said cDNA clone in Table1.

Further preferred is a method for detecting in a biological sample apolypeptide comprising an amino acid sequence which is at least 90%identical to a sequence of at least 10 contiguous amino acids in asequence selected from the group consisting of: an amino acid sequenceof SEQ ID NO:Y wherein Y is any integer as defined in Table 1; and acomplete amino acid sequence of a protein encoded by a human cDNA cloneidentified by a cDNA Clone Identifier in Table 1 and contained in thedeposit with the ATCC Deposit Number shown for said cDNA clone in Table1; which method comprises a step of comparing an amino acid sequence ofat least one polypeptide molecule in said sample with a sequenceselected from said group and determining whether the sequence of saidpolypeptide molecule in said sample is at least 90% identical to saidsequence of at least 10 contiguous amino acids.

Also preferred is the above method wherein said step of comparing anamino acid sequence of at least one polypeptide molecule in said samplewith a sequence selected from said group comprises determining theextent of specific binding of polypeptides in said sample to an antibodywhich binds specifically to a polypeptide comprising an amino acidsequence that is at least 90% identical to a sequence of at least 10contiguous amino acids in a sequence selected from the group consistingof: an amino acid sequence of SEQ ID NO:Y wherein Y is any integer asdefined in Table 1; and a complete amino acid sequence of a proteinencoded by a human cDNA clone identified by a cDNA Clone Identifier inTable 1 and contained in the deposit with the ATCC Deposit Number shownfor said cDNA clone in Table 1.

Also preferred is the above method wherein said step of comparingsequences is performed by comparing the amino acid sequence determinedfrom a polypeptide molecule in said sample with said sequence selectedfrom said group.

Also preferred is a method for identifying the species, tissue or celltype of a biological sample which method comprises a step of detectingpolypeptide molecules in said sample, if any, comprising an amino acidsequence that is at least 90% identical to a sequence of at least 10contiguous amino acids in a sequence selected from the group consistingof: an amino acid sequence of SEQ ID NO:Y wherein Y is any integer asdefined in Table 1; and a complete amino acid sequence of a secretedprotein encoded by a human cDNA clone identified by a cDNA CloneIdentifier in Table 1 and contained in the deposit with the ATCC DepositNumber shown for said cDNA clone in Table 1.

Also preferred is the above method for identifying the species, tissueor cell type of a biological sample, which method comprises a step ofdetecting polypeptide molecules comprising an amino acid sequence in apanel of at least two amino acid sequences, wherein at least onesequence in said panel is at least 90% identical to a sequence of atleast 10 contiguous amino acids in a sequence selected from the abovegroup.

Also preferred is a method for diagnosing in a subject a pathologicalcondition associated with abnormal structure or expression of a geneencoding a secreted protein identified in Table 1, which methodcomprises a step of detecting in a biological sample obtained from saidsubject polypeptide molecules comprising an amino acid sequence in apanel of at least two amino acid sequences, wherein at least onesequence in said panel is at least 90% identical to a sequence of atleast 10 contiguous amino acids in a sequence selected from the groupconsisting of: an amino acid sequence of SEQ ID NO:Y wherein Y is anyinteger as defined in Table 1; and a complete amino acid sequence of asecreted protein encoded by a human cDNA clone identified by a cDNAClone Identifier in Table 1 and contained in the deposit with the ATCCDeposit Number shown for said cDNA clone in Table 1.

In any of these methods, the step of detecting said polypeptidemolecules includes using an antibody.

Also preferred is an isolated nucleic acid molecule comprising anucleotide sequence which is at least 95% identical to a nucleotidesequence encoding a polypeptide wherein said polypeptide comprises anamino acid sequence that is at least 90% identical to a sequence of atleast 10 contiguous amino acids in a sequence selected from the groupconsisting of: an amino acid sequence of SEQ ID NO:Y wherein Y is anyinteger as defined in Table 1; and a complete amino acid sequence of asecreted protein encoded by a human cDNA clone identified by a cDNAClone Identifier in Table 1 and contained in the deposit with the ATCCDeposit Number shown for said cDNA clone in Table 1.

Also preferred is an isolated nucleic acid molecule, wherein saidnucleotide sequence encoding a polypeptide has been optimized forexpression of said polypeptide in a prokaryotic host.

Also preferred is an isolated nucleic acid molecule, wherein saidpolypeptide comprises an amino acid sequence selected from the groupconsisting of: an amino acid sequence of SEQ ID NO:Y wherein Y is anyinteger as defined in Table 1; and a complete amino acid sequence of asecreted protein encoded by a human cDNA clone identified by a cDNAClone Identifier in Table 1 and contained in the deposit with the ATCCDeposit Number shown for said cDNA clone in Table 1.

Further preferred is a method of making a recombinant vector comprisinginserting any of the above isolated nucleic acid molecule into a vector.Also preferred is the recombinant vector produced by this method. Alsopreferred is a method of making a recombinant host cell comprisingintroducing the vector into a host cell, as well as the recombinant hostcell produced by this method.

Also preferred is a method of making an isolated polypeptide comprisingculturing this recombinant host cell under conditions such that saidpolypeptide is expressed and recovering said polypeptide. Also preferredis this method of making an isolated polypeptide, wherein saidrecombinant host cell is a eukaryotic cell and said polypeptide is asecreted portion of a human secreted protein comprising an amino acidsequence selected from the group consisting of: an amino acid sequenceof SEQ ID NO:Y beginning with the residue at the position of the FirstAmino Acid of the Secreted Portion of SEQ ID NO:Y wherein Y is aninteger set forth in Table 1 and said position of the First Amino Acidof the Secreted Portion of SEQ ID NO:Y is defined in Table 1; and anamino acid sequence of a secreted portion of a protein encoded by ahuman cDNA clone identified by a cDNA Clone Identifier in Table 1 andcontained in the deposit with the ATCC Deposit Number shown for saidcDNA clone in Table 1. The isolated polypeptide produced by this methodis also preferred.

Also preferred is a method of treatment of an individual in need of anincreased level of a secreted protein activity, which method comprisesadministering to such an individual a pharmaceutical compositioncomprising an amount of an isolated polypeptide, polynucleotide, orantibody of the claimed invention effective to increase the level ofsaid protein activity in said individual.

Having generally described the invention, the same will be more readilyunderstood by reference to the following examples, which are provided byway of illustration and are not intended as limiting.

EXAMPLES Example 1 Isolation of a Selected cDNA Clone from the DepositedSample

Each cDNA clone in a cited ATCC deposit is contained in a plasmidvector. Table 1 identifies the vectors used to construct the cDNAlibrary from which each clone was isolated. In many cases, the vectorused to construct the library is a phage vector from which a plasmid hasbeen excised. The table immediately below correlates the related plasmidfor each phage vector used in constructing the cDNA library. Forexample, where a particular clone is identified in Table 1 as beingisolated in the vector “Lambda Zap,” the corresponding deposited cloneis in “pBluescript.” Vector Used to Construct Library CorrespondingDeposited Plasmid Lambda Zap pBluescript (pBS) Uni-Zap XR pBluescript(pBS) Zap Express pBK lafmid BA plafmid BA pSport1 pSport1 pCMVSport 2.0pCMVSport 2.0 pCMVSport 3.0 pCMVSport 3.0 pCR ® 2.1 pCR ® 2.1

Vectors Lambda Zap (U.S. Pat. Nos. 5,128,256 and 5,286,636), Uni-Zap XR(U.S. Pat. Nos. 5,128,256 and 5,286,636), Zap Express (U.S. Pat. Nos.5,128,256 and 5,286,636), pBluescript (pBS) (Short, J. M. et al.,Nucleic Acids Res. 16:7583-7600 (1988); Alting-Mees, M. A. and Short, J.M., Nucleic Acids Res. 17:9494 (1989)) and pBK (Alting-Mees, M. A. etal., Strategies 5:58-61 (1992)) are commercially available fromStratagene Cloning Systems, Inc., 11011 N. Torrey Pines Road, La Jolla,Calif., 92037. pBS contains an ampicillin resistance gene and pBKcontains a neomycin resistance gene. Both can be transformed into E.coli strain XL-1 Blue, also available from Stratagene. pBS comes in 4forms SK+, SK−, KS+and KS. The S and K refers to the orientation of thepolylinker to the T7 and T3 primer sequences which flank the polylinkerregion (“S” is for SacI and “K” is for KpnI which are the first sites oneach respective end of the linker). “+” or “−” refer to the orientationof the f1 origin of replication (“ori”), such that in one orientation,single stranded rescue initiated from the f1 ori generates sense strandDNA and in the other, antisense.

Vectors pSport1, pCMVSport 2.0 and pCMVSport 3.0, were obtained fromLife Technologies, Inc., P. O. Box 6009, Gaithersburg, Md. 20897. AllSport vectors contain an ampicillin resistance gene and may betransformed into E. coli strain DH10B, also available from LifeTechnologies. (See, for instance, Gruber, C. E., et al., Focus 15:59(1993).) Vector lafmid BA (Bento Soares, Columbia University, N.Y.)contains an ampicillin resistance gene and can be transformed into E.coli strain XL-1 Blue. Vector pCR®2.1, which is available fromInvitrogen, 1600 Faraday Avenue, Carlsbad, Calif. 92008, contains anampicillin resistance gene and may be transformed into E. coli strainDH10B, available from Life Technologies. (See, for instance, Clark, J.M., Nuc. Acids Res. 16:9677-9686 (1988) and Mead, D. et al.,Bio/Technology 9: (1991).) Preferably, a polynucleotide of the presentinvention does not comprise the phage vector sequences identified forthe particular clone in Table 1, as well as the corresponding plasmidvector sequences designated above.

The deposited material in the sample assigned the ATCC Deposit Numbercited in Table 1 for any given cDNA clone also may contain one or moreadditional plasmids, each comprising a cDNA clone different from thatgiven clone. Thus, deposits sharing the same ATCC Deposit Number containat least a plasmid for each cDNA clone identified in Table 1. Typically,each ATCC deposit sample cited in Table 1 comprises a mixture ofapproximately equal amounts (by weight) of about 50 plasmid DNAs, eachcontaining a different cDNA clone; but such a deposit sample may includeplasmids for more or less than 50 cDNA clones, up to about 500 cDNAclones.

Two approaches can be used to isolate a particular clone from thedeposited sample of plasmid DNAs cited for that clone in Table 1. First,a plasmid is directly isolated by screening the clones using apolynucleotide probe corresponding to SEQ ID NO:X.

Particularly, a specific polynucleotide with 30-40 nucleotides issynthesized using an Applied Biosystems DNA synthesizer according to thesequence reported. The oligonucleotide is labeled, for instance, with³²P-γ-ATP using T4 polynucleotide kinase and purified according toroutine methods. (E.g., Maniatis et al., Molecular Cloning: A LaboratoryManual, Cold Spring Harbor Press, Cold Spring, N.Y. (1982).) The plasmidmixture is transformed into a suitable host, as indicated above (such asXL-1 Blue (Stratagene)) using techniques known to those of skill in theart, such as those provided by the vector supplier or in relatedpublications or patents cited above. The transformants are plated on1.5% agar plates (containing the appropriate selection agent, e.g.,ampicillin) to a density of about 150 transformants (colonies) perplate. These plates are screened using Nylon membranes according toroutine methods for bacterial colony screening (e.g., Sambrook et al.,Molecular Cloning: A Laboratory Manual, 2nd Edit., (1989), Cold SpringHarbor Laboratory Press, pages 1.93 to 1.104), or other techniques knownto those of skill in the art.

Alternatively, two primers of 17-20 nucleotides derived from both endsof the SEQ ID NO:X (i.e., within the region of SEQ ID NO:X bounded bythe 5′ NT and the 3′ NT of the clone defined in Table 1) are synthesizedand used to amplify the desired cDNA using the deposited cDNA plasmid asa template. The polymerase chain reaction is carried out under routineconditions, for instance, in 25 μl of reaction mixture with 0.5 ug ofthe above cDNA template. A convenient reaction mixture is 1.5-5 mMMgCl₂, 0.01% (w/v) gelatin, 20 μM each of dATP, dCTP, dGTP, dTTP, 25pmol of each primer and 0.25 Unit of Taq polymerase. Thirty five cyclesof PCR (denaturation at 94° C. for 1 min; annealing at 55° C. for 1 min;elongation at 72° C. for 1 min) are performed with a Perkin-Elmer Cetusautomated thermal cycler. The amplified product is analyzed by agarosegel electrophoresis and the DNA band with expected molecular weight isexcised and purified. The PCR product is verified to be the selectedsequence by subcloning and sequencing the DNA product.

Several methods are available for the identification of the 5′ or 3′non-coding portions of a gene which may not be present in the depositedclone. These methods include but are not limited to, filter probing,clone enrichment using specific probes, and protocols similar oridentical to 5′ and 3′ “RACE” protocols which are well known in the art.For instance, a method similar to 5′ RACE is available for generatingthe missing 5′ end of a desired full-length transcript. (Fromont-Racineet al., Nucleic Acids Res. 21(7):1683-1684 (1993).)

Briefly, a specific RNA oligonucleotide is ligated to the 5′ ends of apopulation of RNA presumably containing full-length gene RNAtranscripts. A primer set containing a primer specific to the ligatedRNA oligonucleotide and a primer specific to a known sequence of thegene of interest is used to PCR amplify the 5′ portion of the desiredfull-length gene. This amplified product may then be sequenced and usedto generate the full length gene.

This above method starts with total RNA isolated from the desiredsource, although poly-A+ RNA can be used. The RNA preparation can thenbe treated with phosphatase if necessary to eliminate 5′ phosphategroups on degraded or damaged RNA which may interfere with the later RNAligase step. The phosphatase should then be inactivated and the RNAtreated with tobacco acid pyrophosphatase in order to remove the capstructure present at the 5′ ends of messenger RNAs. This reaction leavesa 5′ phosphate group at the 5′ end of the cap cleaved RNA which can thenbe ligated to an RNA oligonucleotide using T4 RNA ligase.

This modified RNA preparation is used as a template for first strandcDNA synthesis using a gene specific oligonucleotide. The first strandsynthesis reaction is used as a template for PCR amplification of thedesired 5′ end using a primer specific to the ligated RNAoligonucleotide and a primer specific to the known sequence of the geneof interest. The resultant product is then sequenced and analyzed toconfirm that the 5′ end sequence belongs to the desired gene.

Example 2 Isolation of Genomic Clones Corresponding to a Polynucleotide

A human genomic P1 library (Genomic Systems, Inc.) is screened by PCRusing primers selected for the cDNA sequence corresponding to SEQ IDNO:X., according to the method described in Example 1. (See also,Sambrook.)

Example 3 Tissue Distribution of Polypeptide

Tissue distribution of mRNA expression of polynucleotides of the presentinvention is determined using protocols for Northern blot analysis,described by, among others, Sambrook et al. For example, a cDNA probeproduced by the method described in Example 1 is labeled with P³² usingthe rediprime™ DNA labeling system (Amersham Life Science), according tomanufacturer's instructions. After labeling, the probe is purified usingCHROMA SPIN-100™ column (Clontech Laboratories, Inc.), according tomanufacturer's protocol number PT1200-1. The purified labeled probe isthen used to examine various human tissues for mRNA expression.

Multiple Tissue Northern (MTN) blots containing various human tissues(H) or human immune system tissues (IM) (Clontech) are examined with thelabeled probe using ExpressHyb™ hybridization solution (Clontech)according to manufacturer's protocol number PT1190-1. Followinghybridization and washing, the blots are mounted and exposed to film at−70° C. overnight, and the films developed according to standardprocedures.

Example 4 Chromosomal Mapping of the Polynucleotides

An oligonucleotide primer set is designed according to the sequence atthe 5′ end of SEQ ID NO:X. This primer preferably spans about 100nucleotides. This primer set is then used in a polymerase chain reactionunder the following set of conditions: 30 seconds, 95° C.; 1 minute, 56°C.; 1 minute, 70° C. This cycle is repeated 32 times followed by one 5minute cycle at 70° C. Human, mouse, and hamster DNA is used as templatein addition to a somatic cell hybrid panel containing individualchromosomes or chromosome fragments (Bios, Inc). The reactions isanalyzed on either 8% polyacrylamide gels or 3.5% agarose gels.Chromosome mapping is determined by the presence of an approximately 100bp PCR fragment in the particular somatic cell hybrid.

Example 5 Bacterial Expression of a Polypeptide

A polynucleotide encoding a polypeptide of the present invention isamplified using PCR oligonucleotide priners corresponding to the 5′ and3′ ends of the DNA sequence, as outlined in Example 1, to synthesizeinsertion fragments. The primers used to amplify the cDNA insert shouldpreferably contain restriction sites, such as BamHI and XbaI, at the 5′end of the primers in order to clone the amplified product into theexpression vector. For example, BamHI and XbaI correspond to therestriction enzyme sites on the bacterial expression vector pQE-9.(Qiagen, Inc., Chatsworth, Calif.). This plasmid vector encodesantibiotic resistance (Amp^(r)), a bacterial origin of replication(ori), an IPTG-regulatable promoter/operator (P/O), a ribosome bindingsite (RBS), a 6-histidine tag (6-His), and restriction enzyme cloningsites.

The pQE-9 vector is digested with BamHI and XbaI and the amplifiedfragment is ligated into the pQE-9 vector maintaining the reading frameinitiated at the bacterial RBS. The ligation mixture is then used totransform the E. coli strain M15/rep4 (Qiagen, Inc.) which containsmultiple copies of the plasmid pREP4, which expresses the lacI repressorand also confers kanamycin resistance (Kan^(r)). Transformants areidentified by their ability to grow on LB plates andampicillin/kanamycin resistant colonies are selected. Plasmid DNA isisolated and confirmed by restriction analysis.

Clones containing the desired constructs are grown overnight (O/N) inliquid culture in LB media supplemented with both Amp (100 ug/ml) andKan (25 ug/ml). The O/N culture is used to inoculate a large culture ata ratio of 1:100 to 1:250. The cells are grown to an optical density 600(O.D.⁶⁰⁰) of between 0.4 and 0.6. IPTG (Isopropyl-B-D-thiogalactopyranoside) is then added to a final concentration of 1 mM. IPTG inducesby inactivating the lacI repressor, clearing the P/O leading toincreased gene expression.

Cells are grown for an extra 3 to 4 hours. Cells are then harvested bycentrifugation (20 mins at 6000×g). The cell pellet is solubilized inthe chaotropic agent 6 Molar Guanidine HCl by stirring for 3-4 hours at4° C. The cell debris is removed by centrifugation, and the supernatantcontaining the polypeptide is loaded onto a nickel-nitrilo-tri-aceticacid (“Ni—NTA”) affinity resin column (available from QIAGEN, Inc.,supra). Proteins with a 6× His tag bind to the Ni—NTA resin with highaffinity and can be purified in a simple one-step procedure (for detailssee: The QIAexpressionist (1995) QIAGEN, Inc., supra).

Briefly, the supernatant is loaded onto the column in 6 M guanidine-HCl,pH 8, the column is first washed with 10 volumes of 6 M guanidine-HCl,pH 8, then washed with 10 volumes of 6 M guanidine-HCl pH 6, and finallythe polypeptide is eluted with 6 M guanidine-HCl, pH 5.

The purified protein is then renatured by dialyzing it againstphosphate-buffered saline (PBS) or 50 mM Na-acetate, pH 6 buffer plus200 mM NaCl. Alternatively, the protein can be successfully refoldedwhile immobilized on the Ni—NTA column. The recommended conditions areas follows: renature using a linear 6M-1M urea gradient in 500 mM NaCl,20% glycerol, 20 mM Tris/HCl pH 7.4, containing protease inhibitors. Therenaturation should be performed over a period of 1.5 hours or more.After renaturation the proteins are eluted by the addition of 250 mMimmidazole. Immidazole is removed by a final dialyzing step against PBSor 50 mM sodium acetate pH 6 buffer plus 200 mM NaCl. The purifiedprotein is stored at 4° C. or frozen at −80° C.

In addition to the above expression vector, the present inventionfurther includes an expression vector comprising phage operator andpromoter elements operatively linked to a polynucleotide of the presentinvention, called pHE4a. (ATCC Accession Number 209645, deposited onFeb. 25, 1998.) This vector contains: 1) a neomycinphosphotransferasegene as a selection marker, 2) an E. coli origin of replication, 3) a T5phage promoter sequence, 4) two lac operator sequences, 5) aShine-Delgarno sequence, and 6) the lactose operon repressor gene(lacIq). The origin of replication (oriC) is derived from pUC19 (LTI,Gaithersburg, Md.). The promoter sequence and operator sequences aremade synthetically.

DNA can be inserted into the pHEa by restricting the vector with NdeIand XbaI, BamHI, XhoI, or Asp718, running the restricted product on agel, and isolating the larger fragment (the stuffer fragment should beabout 310 base pairs). The DNA insert is generated according to the PCRprotocol described in Example 1, using PCR primers having restrictionsites for NdeI (5′ primer) and XbaI, BamHI, XhoI, or Asp718 (3′ primer).The PCR insert is gel purified and restricted with compatible enzymes.The insert and vector are ligated according to standard protocols.

The engineered vector could easily be substituted in the above protocolto express protein in a bacterial system.

Example 6 Purification of a Polypeptide from an Inclusion Body

The following alternative method can be used to purify a polypeptideexpressed in E. coli when it is present in the form of inclusion bodies.Unless otherwise specified, all of the following steps are conducted at4-10° C.

Upon completion of the production phase of the E. coli fermentation, thecell culture is cooled to 4-10° C. and the cells harvested by continuouscentrifugation at 15,000 rpm (Heraeus Sepatech). On the basis of theexpected yield of protein per unit weight of cell paste and the amountof purified protein required, an appropriate amount of cell paste, byweight, is suspended in a buffer solution containing 100 mM Tris, 50 mMEDTA, pH 7.4. The cells are dispersed to a homogeneous suspension usinga high shear mixer.

The cells are then lysed by passing the solution through amicrofluidizer (Microfuidics, Corp. or APV Gaulin, Inc.) twice at4000-6000 psi. The homogenate is then mixed with NaCl solution to afinal concentration of 0.5 M NaCl, followed by centrifugation at 7000×g15 min. The resultant pellet is washed again using 0.5M NaCl, 100 mMTris, 50 mM EDTA, pH 7.4.

The resulting washed inclusion bodies are solubilized with 1.5 Mguanidine hydrochloride (GuHCl) for 2-4 hours. After 7000×gcentrifugation for 15 min., the pellet is discarded and the polypeptidecontaining supernatant is incubated at 4° C. overnight to allow furtherGuHCl extraction.

Following high speed centrifugation (30,000×g) to remove insolubleparticles, the GuHCl solubilized protein is refolded by quickly mixingthe GuHCl extract with 20 volumes of buffer containing 50 mM sodium, pH4.5, 150 mM NaCl, 2 mM EDTA by vigorous stirring. The refolded dilutedprotein solution is kept at 4° C. without mixing for 12 hours prior tofurther purification steps.

To clarify the refolded polypeptide solution, a previously preparedtangential filtration unit equipped with 0.16 μm membrane filter withappropriate surface area (e.g., Filtron), equilibrated with 40 mM sodiumacetate, pH 6.0 is employed. The filtered sample is loaded onto a cationexchange resin (e.g., Poros HS-50, Perseptive Biosystems). The column iswashed with 40 mM sodium acetate, pH 6.0 and eluted with 250 mM, 500 mM,1000 mM, and 1500 mM NaCl in the same buffer, in a stepwise manner. Theabsorbance at 280 nm of the effluent is continuously monitored.Fractions are collected and further analyzed by SDS-PAGE.

Fractions containing the polypeptide are then pooled and mixed with 4volumes of water. The diluted sample is then loaded onto a previouslyprepared set of tandem columns of strong anion (Poros HQ-50, PerseptiveBiosystems) and weak anion (Poros CM-20, Perseptive Biosystems) exchangeresins. The columns are equilibrated with 40 mM sodium acetate, pH 6.0.Both columns are washed with 40 mM sodium acetate, pH 6.0, 200 mM NaCl.The CM-20 column is then eluted using a 10 column volume linear gradientranging from 0.2 M NaCl, 50 mM sodium acetate, pH 6.0 to 1.0 M NaCl, 50mM sodium acetate, pH 6.5. Fractions are collected under constant A₂₈₀monitoring of the effluent. Fractions containing the polypeptide(determined, for instance, by 16% SDS-PAGE) are then pooled.

The resultant polypeptide should exhibit greater than 95% purity afterthe above refolding and purification steps. No major contaminant bandsshould be observed from Commassie blue stained 16% SDS-PAGE gel when 5μg of purified protein is loaded. The purified protein can also betested for endotoxin/LPS contamination, and typically the LPS content isless than 0.1 ng/ml according to LAL assays.

Example 7 Cloning and Expression of a Polypeptide in a BaculovirusExpression System

In this example, the plasmid shuttle vector pA2 is used to insert apolynucleotide into a baculovirus to express a polypeptide. Thisexpression vector contains the strong polyhedrin promoter of theAutographa californica nuclear polyhedrosis virus (AcMNPV) followed byconvenient restriction sites such as BamHI, Xba I and Asp718. Thepolyadenylation site of the simian virus 40 (“SV40”) is used forefficient polyadenylation. For easy selection of recombinant virus, theplasmid contains the beta-galactosidase gene from E. coli under controlof a weak Drosophila promoter in the same orientation, followed by thepolyadenylation signal of the polyhedrin gene. The inserted genes areflanked on both sides by viral sequences for cell-mediated homologousrecombination with wild-type viral DNA to generate a viable virus thatexpress the cloned polynucleotide.

Many other baculovirus vectors can be used in place of the vector above,such as pAc373, pVL941, and pAcIM1, as one skilled in the art wouldreadily appreciate, as long as the construct provides appropriatelylocated signals for transcription, translation, secretion and the like,including a signal peptide and an in-frame AUG as required. Such vectorsare described, for instance, in Luckow et al., Virology 170:31-39(1989).

Specifically, the cDNA sequence contained in the deposited clone,including the AUG initiation codon and the naturally associated leadersequence identified in Table 1, is amplified using the PCR protocoldescribed in Example 1. If the naturally occurring signal sequence isused to produce the secreted protein, the pA2 vector does not need asecond signal peptide. Alternatively, the vector can be modified (pA2GP) to include a baculovirus leader sequence, using the standard methodsdescribed in Summers et al., “A Manual of Methods for BaculovirusVectors and Insect Cell Culture Procedures,” Texas AgriculturalExperimental Station Bulletin No. 1555 (1987).

The amplified fragment is isolated from a 1% agarose gel using acommercially available kit (“Geneclean,” BIO 101 Inc., La Jolla,Calif.). The fragment then is digested with appropriate restrictionenzymes and again purified on a 1% agarose gel.

The plasmid is digested with the corresponding restriction enzymes andoptionally, can be dephosphorylated using calf intestinal phosphatase,using routine procedures known in the art. The DNA is then isolated froma 1% agarose gel using a commercially available kit (“Geneclean” BIO 101Inc., La Jolla, Calif.).

The fragment and the dephosphorylated plasmid are ligated together withT4 DNA ligase. E. coli HB101 or other suitable E. coli hosts such asXL-1 Blue (Stratagene Cloning Systems, La Jolla, Calif.) cells aretransformed with the ligation mixture and spread on culture plates.Bacteria containing the plasmid are identified by digesting DNA fromindividual colonies and analyzing the digestion product by gelelectrophoresis. The sequence of the cloned fragment is confirmed by DNAsequencing.

Five μg of a plasmid containing the polynucleotide is co-transfectedwith 1.0 μg of a commercially available linearized baculovirus DNA(“BaculoGold™ baculovirus DNA”, Pharmingen, San Diego, Calif.), usingthe lipofection method described by Felgner et al., Proc. Natl. Acad.Sci. USA 84:7413-7417 (1987). One μg of BaculoGold™ virus DNA and 5 μgof the plasmid are mixed in a sterile well of a microtiter platecontaining 50 μl of serum-free Grace's medium (Life Technologies Inc.,Gaithersburg, Md.). Afterwards, 10 μl Lipofectin plus 90 μl Grace'smedium are added, mixed and incubated for 15 minutes at roomtemperature. Then the transfection mixture is added drop-wise to Sf9insect cells (ATCC CRL 1711) seeded in a 35 mm tissue culture plate with1 ml Grace's medium without serum. The plate is then incubated for 5hours at 27° C. The transfection solution is then removed from the plateand 1 ml of Grace's insect medium supplemented with 10% fetal calf serumis added. Cultivation is then continued at 27° C. for four days.

After four days the supernatant is collected and a plaque assay isperformed, as described by Summers and Smith, supra. An agarose gel with“Blue Gal” (Life Technologies Inc., Gaithersburg) is used to allow easyidentification and isolation of gal-expressing clones, which produceblue-stained plaques. (A detailed description of a “plaque assay” ofthis type can also be found in the user's guide for insect cell cultureand baculovirology distributed by Life Technologies Inc., Gaithersburg,page 9-10.) After appropriate incubation, blue stained plaques arepicked with the tip of a micropipettor (e.g., Eppendorf). The agarcontaining the recombinant viruses is then resuspended in amicrocentrifuge tube containing 200 μl of Grace's medium and thesuspension containing the recombinant baculovirus is used to infect Sf9cells seeded in 35 mm dishes. Four days later the supernatants of theseculture dishes are harvested and then they are stored at 4° C.

To verify the expression of the polypeptide, Sf9 cells are grown inGrace's medium supplemented with 10% heat-inactivated FBS. The cells areinfected with the recombinant baculovirus containing the polynucleotideat a multiplicity of infection (“MOI”) of about 2. If radiolabeledproteins are desired, 6 hours later the medium is removed and isreplaced with SF900 II medium minus methionine and cysteine (availablefrom Life Technologies Inc., Rockville, Md.). After 42 hours, 5 μCi of³⁵S-methionine and 5 μCi ³⁵S-cysteine (available from Amersham) areadded. The cells are further incubated for 16 hours and then areharvested by centrifugation. The proteins in the supernatant as well asthe intracellular proteins are analyzed by SDS-PAGE followed byautoradiography (if radiolabeled).

Microsequencing of the amino acid sequence of the amino terminus ofpurified protein may be used to determine the amino terminal sequence ofthe produced protein.

Example 8 Expression of a Polypeptide in Mammalian Cells

The polypeptide of the present invention can be expressed in a mammaliancell. A typical mammalian expression vector contains a promoter element,which mediates the initiation of transcription of mRNA, a protein codingsequence, and signals required for the termination of transcription andpolyadenylation of the transcript. Additional elements includeenhancers, Kozak sequences and intervening sequences flanked by donorand acceptor sites for RNA splicing. Highly efficient transcription isachieved with the early and late promoters from SV40, the long terminalrepeats (LTRs) from Retroviruses, e.g., RSV, HTLVI, HIVI and the earlypromoter of the cytomegalovirus (CMV). However, cellular elements canalso be used (e.g., the human actin promoter).

Suitable expression vectors for use in practicing the present inventioninclude, for example, vectors such as pSVL and pMSG (Pharmacia, Uppsala,Sweden), pRSVcat (ATCC 37152), pSV2dhfr (ATCC 37146), pBC12MI (ATCC67109), pCMVSport 2.0, and pCMVSport 3.0. Mammalian host cells thatcould be used include, human Hela, 293, H9 and Jurkat cells, mouseNIH3T3 and C127 cells, Cos 1, Cos 7 and CV1, quail QC1-3 cells, mouse Lcells and Chinese hamster ovary (CHO) cells.

Alternatively, the polypeptide can be expressed in stable cell linescontaining the polynucleotide integrated into a chromosome. Theco-transfection with a selectable marker such as dhfr, gpt, neomycin,hygromycin allows the identification and isolation of the transfectedcells.

The transfected gene can also be amplified to express large amounts ofthe encoded protein. The DHFR (dihydrofolate reductase) marker is usefulin developing cell lines that carry several hundred or even severalthousand copies of the gene of interest. (See, e.g., Alt, F. W., et al.,J. Biol. Chem. 253:1357-1370 (1978); Hamlin, J. L. and Ma, C., Biochem.et Biophys. Acta, 1097:107-143 (1990); Page, M. J. and Sydenham, M. A.,Biotechnology 9:64-68 (1991).) Another useful selection marker is theenzyme glutamine synthase (GS) (Murphy et al., Biochem J. 227:277-279(1991); Bebbington et al., Bio/Technology 10:169-175 (1992). Using thesemarkers, the mammalian cells are grown in selective medium and the cellswith the highest resistance are selected. These cell lines contain theamplified gene(s) integrated into a chromosome. Chinese hamster ovary(CHO) and NSO cells are often used for the production of proteins.

Derivatives of the plasmid pSV2-dhfr (ATCC Accession No. 37146), theexpression vectors pC4 (ATCC Accession No. 209646) and pC6 (ATCCAccession No.209647) contain the strong promoter (LTR) of the RousSarcoma Virus (Cullen et al., Molecular and Cellular Biology, 438-447(March, 1985)) plus a fragment of the CMV-enhancer (Boshart et al., Cell41:521-530 (1985).) Multiple cloning sites, e.g., with the restrictionenzyme cleavage sites BamHI, XbaI and Asp718, facilitate the cloning ofthe gene of interest. The vectors also contain the 3′ intron, thepolyadenylation and termination signal of the rat preproinsulin gene,and the mouse DHFR gene under control of the SV40 early promoter.

Specifically, the plasmid pC6, for example, is digested with appropriaterestriction enzymes and then dephosphorylated using calf intestinalphosphates by procedures known in the art. The vector is then isolatedfrom a 1% agarose gel.

A polynucleotide of the present invention is amplified according to theprotocol outlined in Example 1. If the naturally occurring signalsequence is used to produce the secreted protein, the vector does notneed a second signal peptide. Alternatively, if the naturally occurringsignal sequence is not used, the vector can be modified to include aheterologous signal sequence. (See, e.g., WO 96/34891.)

The amplified fragment is isolated from a 1% agarose gel using acommercially available kit (“Geneclean,” BIO 101 Inc., La Jolla,Calif.). The fragment then is digested with appropriate restrictionenzymes and again purified on a 1% agarose gel.

The amplified fragment is then digested with the same restriction enzymeand purified on a 1% agarose gel. The isolated fragment and thedephosphorylated vector are then ligated with T4 DNA ligase. E. coliHB101 or XL-1 Blue cells are then transformed and bacteria areidentified that contain the fragment inserted into plasmid pC6 using,for instance, restriction enzyme analysis.

Chinese hamster ovary cells lacking an active DBFR gene is used fortransfection. Five μg of the expression plasmid pC6 is cotransfectedwith 0.5 μg of the plasmid pSVneo using lipofectin (Felgner et al.,supra). The plasmid pSV2-neo contains a dominant selectable marker, theneo gene from Tn5 encoding an enzyme that confers resistance to a groupof antibiotics including G418. The cells are seeded in alpha minus MEMsupplemented with 1 mg/ml G418. After 2 days, the cells are trypsinizedand seeded in hybridoma cloning plates (Greiner, Germany) in alpha minusMEM supplemented with 10, 25, or 50 ng/ml of metothrexate plus 1 mg/mlG418. After about 10-14 days single clones are trypsinized and thenseeded in 6-well petri dishes or 10 ml flasks using differentconcentrations of methotrexate (50 nM, 100 nM, 200 nM, 400 nM, 800 nM).Clones growing at the highest concentrations of methotrexate are thentransferred to new 6-well plates containing even higher concentrationsof methotrexate (1 μM, 2 μM, 5 μM, 10 mM, 20 mM). The same procedure isrepeated until clones are obtained which grow at a concentration of100-200 μM. Expression of the desired gene product is analyzed, forinstance, by SDS-PAGE and Western blot or by reversed phase HPLCanalysis.

Example 9 Protein Fusions

The polypeptides of the present invention are preferably fused to otherproteins. These fusion proteins can be used for a variety ofapplications. For example, fusion of the present polypeptides toHis-tag, HA-tag, protein A, IgG domains, and maltose binding proteinfacilitates purification. (See Example 5; see also EP A 394,827;Traunecker, et al., Nature 331:84-86 (1988).) Similarly, fusion toIgG-1, IgG-3, and albumin increases the halflife time in vivo. Nuclearlocalization signals fused to the polypeptides of the present inventioncan target the protein to a specific subcellular localization, whilecovalent heterodimer or homodimers can increase or decrease the activityof a fusion protein. Fusion proteins can also create chimeric moleculeshaving more than one function. Finally, fusion proteins can increasesolubility and/or stability of the fused protein compared to thenon-fused protein. All of the types of fusion proteins described abovecan be made by modifying the following protocol, which outlines thefusion of a polypeptide to an IgG molecule, or the protocol described inExample 5.

Briefly, the human Fc portion of the IgG molecule can be PCR amplified,using primers that span the 5′ and 3′ ends of the sequence describedbelow. These primers also should have convenient restriction enzymesites that will facilitate cloning into an expression vector, preferablya mammalian expression vector.

For example, if pC4 (Accession No. 209646) is used, the human Fc portioncan be ligated into the BamHI cloning site. Note that the 3′ BamHI siteshould be destroyed. Next, the vector containing the human Fc portion isre-restricted with BamHI, linearizing the vector, and a polynucleotideof the present invention, isolated by the PCR protocol described inExample 1, is ligated into this BamHI site. Note that the polynucleotideis cloned without a stop codon, otherwise a fusion protein will not beproduced.

If the naturally occurring signal sequence is used to produce thesecreted protein, pC4 does not need a second signal peptide.Alternatively, if the naturally occurring signal sequence is not used,the vector can be modified to include a heterologous signal sequence.(See, e.g., WO 96/34891.)

Human IgG Fc region: (SEQ ID NO:1)GGGATCCGGAGCCCAAATCTTCTGACAAAACTCACACATGCCCACCGTGCCCAGCACCTGAATTCGAGGGTGCACCGTCAGTCTTCCTCTTCCCCCCAAAACCCAAGGACACCCTCATGATCTCCCGGACTCCTGAGGTCACATGCGTGGTGGTGGACGTAAGCCACGAAGACCCTGAGGTCAAGTTCAACTGGTACGTGGACGGCGTGGAGGTGCATAATGCCAAGACAAAGCCGCGGGAGGAGCAGTACAACAGCACGTACCGTGTGGTCAGCGTCCTCACCGTCCTGCACCAGGACTGGCTGAATGGCAAGGAGTACAAGTGCAAGGTCTCCAACAAAGCCCTCCCAACCCCCATCGAGAAAACCATCTCCAAAGCCAAAGGGCAGCCCCGAGAACCACAGGTGTACACCCTGCCCCCATCCCGGGATGAGCTGACCAAGAACCAGGTCAGCCTGACCTGCCTGGTCAAAGGCTTCTATCCAAGCGACATCGCCGTGGAGTGGGAGAGCAATGGGCAGCCGGAGAACAACTACAAGACCACGCCTCCCGTGCTGGACTCCGACGGCTCCTTCTTCCTCTACAGCAAGCTCACCGTGGACAAGAGCAGGTGGCAGCAGGGGAACGTCTTCTCATGCTCCGTGATGCATGAGGCTCTGCACAACCACTACACGCAGAAGAGCCTCTCCCTGTCTCCGGGTAAATGAGTGCGACGGCCGCGACTCTAGAGGAT

Example 10 Production of an Antibody from a Polypeptide

The antibodies of the present invention can be prepared by a variety ofmethods. (See, Current Protocols, Chapter 2.) For example, cellsexpressing a polypeptide of the present invention is administered to ananimal to induce the production of sera containing polyclonalantibodies. In a preferred method, a preparation of the secreted proteinis prepared and purified to render it substantially free of naturalcontaminants. Such a preparation is then introduced into an animal inorder to produce polyclonal antisera of greater specific activity.

In the most preferred method, the antibodies of the present inventionare monoclonal antibodies (or protein binding fragments thereof). Suchmonoclonal antibodies can be prepared using hybridoma technology.(Köhler et al., Nature 256:495 (1975); Köhler et al., Eur. J. Immunol.6:511 (1976); Köhler et al., Eur. J. Immunol. 6:292 (1976); Hammerlinget al., in: Monoclonal Antibodies and T-Cell Hybridomas, Elsevier, N.Y.,pp. 563-681 (1981).) In general, such procedures involve immunizing ananimal (preferably a mouse) with polypeptide or, more preferably, with asecreted polypeptide-expressing cell. Such cells may be cultured in anysuitable tissue culture medium; however, it is preferable to culturecells in Earle's modified Eagle's medium supplemented with 10% fetalbovine serum (inactivated at about 56° C.), and supplemented with about10 g/l of nonessential amino acids, about 1,000 U/ml of penicillin, andabout 100 μg/ml of streptomycin.

The splenocytes of such mice are extracted and fused with a suitablemyeloma cell line. Any suitable myeloma cell line may be employed inaccordance with the present invention; however, it is preferable toemploy the parent myeloma cell line (SP2O), available from the ATCC.After fusion, the resulting hybridoma cells are selectively maintainedin HAT medium, and then cloned by limiting dilution as described byWands et al. (Gastroenterology 80:225-232 (1981).) The hybridoma cellsobtained through such a selection are then assayed to identify cloneswhich secrete antibodies capable of binding the polypeptide.

Alternatively, additional antibodies capable of binding to thepolypeptide can be produced in a two-step procedure using anti-idiotypicantibodies. Such a method makes use of the fact that antibodies arethemselves antigens, and therefore, it is possible to obtain an antibodywhich binds to a second antibody. In accordance with this method,protein specific antibodies are used to immunize an animal, preferably amouse. The splenocytes of such an animal are then used to producehybridoma cells, and the hybridoma cells are screened to identify cloneswhich produce an antibody whose ability to bind to the protein-specificantibody can be blocked by the polypeptide. Such antibodies compriseanti-idiotypic antibodies to the protein-specific antibody and can beused to immunize an animal to induce formation of furtherprotein-specific antibodies.

It will be appreciated that Fab and F(ab′)2 and other fragments of theantibodies of the present invention may be used according to the methodsdisclosed herein. Such fragments are typically produced by proteolyticcleavage, using enzymes such as papain (to produce Fab fragments) orpepsin (to produce F(ab′)2 fragments). Alternatively, secretedprotein-binding fragments can be produced through the application ofrecombinant DNA technology or through synthetic chemistry.

For in vivo use of antibodies in humans, it may be preferable to use“humanized” chimeric monoclonal antibodies. Such antibodies can beproduced using genetic constructs derived from hybridoma cells producingthe monoclonal antibodies described above. Methods for producingchimeric antibodies are known in the art. (See, for review, Morrison,Science 229:1202 (1985); Oi et al., BioTechniques 4:214 (1986); Cabillyet al., U.S. Pat. No. 4,816,567; Taniguchi et al., EP 171496; Morrisonet al., EP 173494; Neuberger et al., WO 8601533; Robinson et al., WO8702671; Boulianne et al., Nature 312:643 (1984); Neuberger et al.,Nature 314:268 (1985).)

Example 11 Production of Secreted Protein for High-Throughput ScreeningAssays

The following protocol produces a supernatant containing a polypeptideto be tested. This supernatant can then be used in the Screening Assaysdescribed in Examples 13-20.

First, dilute Poly-D-Lysine (644 587 Boehringer-Mannheim) stock solution(1 mg/ml in PBS) 1:20 in PBS (w/o calcium or magnesium 17-516FBiowhittaker) for a working solution of 50 ug/ml. Add 200 ul of thissolution to each well (24 well plates) and incubate at RT for 20minutes. Be sure to distribute the solution over each well (note: a12-channel pipetter may be used with tips on every other channel).Aspirate off the Poly-D-Lysine solution and rinse with 1 ml PBS(Phosphate Buffered Saline). The PBS should remain in the well untiljust prior to plating the cells and plates may be poly-lysine coated inadvance for up to two weeks.

Plate 293T cells (do not carry cells past P+20) at 2×10⁵ cells/well in0.5 ml DMEM (Dulbecco's Modified Eagle Medium) (with 4.5 G/L glucose andL-glutamine (12-604F Biowhittaker))/10% heat inactivated FBS (14-503FBiowhittaker)/1× Penstrep (17-602E Biowhittaker). Let the cells growovernight.

The next day, mix together in a sterile solution basin: 300 ulLipofectamine (18324-012 Gibco/BRL) and 5 ml Optimem I (31985070Gibco/BRL)/96-well plate. With a small volume multi-channel pipetter,aliquot approximately 2 ug of an expression vector containing apolynucleotide insert, produced by the methods described in Examples 8or 9, into an appropriately labeled 96-well round bottom plate. With amulti-channel pipetter, add 50 ul of the Lipofectamine/Optimem I mixtureto each well. Pipette up and down gently to mix. Incubate at RT 15-45minutes. After about 20 minutes, use a multi-channel pipetter to add 150ul Optimem I to each well. As a control, one plate of vector DNA lackingan insert should be transfected with each set of transfections.

Preferably, the transfection should be performed by tag-teaming thefollowing tasks. By tag-teaming, hands on time is cut in half, and thecells do not spend too much time on PBS. First, person A aspirates offthe media from four 24-well plates of cells, and then person B rinseseach well with 0.5-1 ml PBS. Person A then aspirates off PBS rinse, andperson B, using a12-channel pipetter with tips on every other channel,adds the 200 ul of DNA/Lipofectamine/Optimem I complex to the odd wellsfirst, then to the even wells, to each row on the 24-well plates.Incubate at 37° C. for 6 hours.

While cells are incubating, prepare appropriate media, either 1% BSA inDMEM with 1× penstrep, or CHO-5 media (116.6 mg/L of CaCl2 (anhyd);0.00130 mg/L CuSO₄-5H₂0; 0.050 mg/L of Fe(NO₃)₃-9H₂O; 0.417 mg/L ofFeSO₄-7H₂O; 311.80 mg/L of Kc1; 28.64 mg/L of MgCl₂; 48.84 mg/L ofMgSO₄; 6995.50 mg/L of NaCl; 2400.0 mg/L of NaHCO₃; 62.50 mg/L ofNaH₂PO₄-H₂0; 71.02 mg/L of Na₂HPO4; 0.4320 mg/L of ZnSO₄-7H₂O; 0.002mg/L of Arachidonic Acid; 1.022 mg/L of Cholesterol; 0.070 mg/L ofDL-alpha-Tocopherol-Acetate; 0.0520 mg/L of Linoleic Acid; 0.010 mg/L ofLinolenic Acid; 0.010 mg/L of Myristic Acid; 0.010 mg/L of Oleic Acid;0.010 mg/L of Palmitric Acid; 0.010 mg/L of Palmitic Acid; 100 mg/L ofPluronic F-68; 0.010 mg/L of Stearic Acid; 2.20 mg/L of Tween 80; 4551mg/L of D-Glucose; 130.85 mg/ml of L-Alanine; 147.50 mg/ml ofL-Arginine-HCL; 7.50 mg/ml of L-Asparagine-H₂0; 6.65 mg/ml of L-AsparticAcid; 29.56 mg/ml of L-Cystine-2HCL-H₂0; 31.29 mg/ml of L-Cystine-2HCL;7.35 mg/ml of L-Glutamic Acid; 365.0 mg/ml of L-Glutamine; 18.75 mg/mlof Glycine; 52.48 mg/ml of L-Histidine-HCL-H₂0; 106.97 mg/ml ofL-Isoleucine; 111.45 mg/ml of L-Leucine; 163.75 mg/ml of L-Lysine HCL;32.34 mg/ml of L-Methionine; 68.48 mg/ml of L-Phenylalainine; 40.0 mg/mlof L-Proline; 26.25 mg/ml of L-Serine; 101.05 mg/ml of L-Threonine;19.22 mg/ml of L-Tryptophan; 91.79 mg/ml of L-Tryrosine-2Na-2H₂0; 99.65mg/ml of L-Valine; 0.0035 mg/L of Biotin; 3.24 mg/L of D-CaPantothenate; 11.78 mg/L of Choline Chloride; 4.65 mg/L of Folic Acid;15.60 mg/L of i-Inositol; 3.02 mg/L of Niacinamide; 3.00 mg/L ofPyridoxal HCL; 0.031 mg/L of Pyridoxine HCL; 0.319 mg/L of Riboflavin;3.17 mg/L of Thiamine HCL; 0.365 mg/L of Thymidine; and 0.680 mg/L ofVitamin B₁₂; 25 mM of HEPES Buffer; 2.39 mg/L of Na Hypoxanthine; 0.105mg/L of Lipoic Acid; 0.081 mg/L of Sodium Putrescine-2HCL; 55.0 mg/L ofSodium Pyruvate; 0.0067 mg/L of Sodium Selenite; 20 uM of Ethanolamine;0.122 mg/L of Ferric Citrate; 41.70 mg/L of Methyl-B-Cyclodextrincomplexed with Linoleic Acid; 33.33 mg/L of Methyl-B-Cyclodextrincomplexed with Oleic Acid; and 10 mg/L of Methyl-B-Cyclodextrincomplexed with Retinal) with 2 mm glutamine and 1× penstrep. (BSA(81-068-3 Bayer) 100 gm dissolved in 1L DMEM for a 10% BSA stocksolution). Filter the media and collect 50 ul for endotoxin assay in 15ml polystyrene conical.

The transfection reaction is terminated, preferably by tag-teaming, atthe end of the incubation period. Person A aspirates off thetransfection media, while person B adds 1.5 ml appropriate media to eachwell. Incubate at 37° C. for 45 or 72 hours depending on the media used:1% BSA for 45 hours or CHO-5 for 72 hours.

On day four, using a 300 ul multichannel pipetter, aliquot 600ul in one1 ml deep well plate and the remaining supernatant into a 2 ml deepwell. The supernatants from each well can then be used in the assaysdescribed in Examples 13-20.

It is specifically understood that when activity is obtained in any ofthe assays described below using a supernatant, the activity originatesfrom either the polypeptide directly (e.g., as a secreted protein) or bythe polypeptide inducing expression of other proteins, which are thensecreted into the supernatant. Thus, the invention further provides amethod of identifying the protein in the supernatant characterized by anactivity in a particular assay.

Example 12 Construction of GAS Reporter Construct

One signal transduction pathway involved in the differentiation andproliferation of cells is called the Jaks-STATs pathway. Activatedproteins in the Jaks-STATs pathway bind to gamma activation site “GAS”elements or interferon-sensitive responsive element (“ISRE”), located inthe promoter of many genes. The binding of a protein to these elementsalter the expression of the associated gene.

GAS and ISRE elements are recognized by a class of transcription factorscalled Signal Transducers and Activators of Transcription, or “STATs.”There are six members of the STATs family. Stat1 and Stat3 are presentin many cell types, as is Stat2 (as response to IFN-alpha iswidespread). Stat4 is more restricted and is not in many cell typesthough it has been found in T helper class I, cells after treatment withIL-12. Stat5 was originally called mammary growth factor, but has beenfound at higher concentrations in other cells including myeloid cells.It can be activated in tissue culture cells by many cytokines.

The STATs are activated to translocate from the cytoplasm to the nucleusupon tyrosine phosphorylation by a set of kinases known as the JanusKinase (“Jaks”) family. Jaks represent a distinct family of solubletyrosines kinases and include Tyk2, Jak1, Jak2, and Jak3. These kinasesdisplay significant sequence similarity and are generally catalyticallyinactive in resting cells.

The Jaks are activated by a wide range of receptors summarized in theTable below. (Adapted from review by Schidler and Darnell, Ann. Rev.Biochem. 64:621-51 (1995).) A cytokine receptor family, capable ofactivating Jaks, is divided into two groups: (a) Class 1 includesreceptors for IL-2, IL-3, IL-4, IL-6, IL-7, IL-9, IL-11, IL-12, IL-15,Epo, PRL, GH, G-CSF, GM-CSF, LIF, CNTF, and thrombopoietin; and (b)Class 2 includes IFN-a, IFN-g, and IL-10. The Class 1 receptors share aconserved cysteine motif (a set of four conserved cysteines and onetryptophan) and a WSXWS motif (a membrane proxial region encodingTrp-Ser-Xxx-Trp-Ser (SEQ ID NO:2)).

Thus, on binding of a ligand to a receptor, Jaks are activated, which inturn activate STATs, which then translocate and bind to GAS elements.This entire process is encompassed in the Jaks-STATs signal transductionpathway.

Therefore, activation of the Jaks-STATs pathway, reflected by thebinding of the GAS or the ISRE element, can be used to indicate proteinsinvolved in the proliferation and differentiation of cells. For example,growth factors and cytokines are known to activate the Jaks-STATspathway. (See Table below.) Thus, by using GAS elements linked toreporter molecules, activators of the Jaks-STATs pathway can beidentified. JAKs Ligand tyk2 Jak1 Jak2 Jak3 STATS GAS (elements) or ISREIFN family IFN-a/B + + − − 1, 2, 3 ISRE IFN-g + + − 1 GAS (IRF1 > Lys6 >IFP) Il-10 + ? ? − 1, 3 gp130 family IL-6 (Pleiotrohic) + + + ? 1, 3 GAS(IRF1 > Lys6 > IFP) Il-11 (Pleiotrohic) ? + ? ? 1, 3 OnM (Pleiotrohic)? + + ? 1, 3 LIF (Pleiotrohic) ? + + ? 1, 3 CNTF (Pleiotrohic) −/+ + + ?1, 3 G-CSF (Pleiotrohic) ? + ? ? 1, 3 IL-12 (Pleiotrohic) + − + + 1, 3g-C family IL-2 (lymphocytes) − + − + 1, 3, 5 GAS IL-4 (lymph/myeloid)− + − + 6 GAS (IRF1 = IFP >> Ly6) (IgH) IL-7 (lymphocytes) − + − + 5 GASIL-9 (lymphocytes) − + − + 5 GAS IL-13 (lymphocyte) − + ? ? 6 GAS IL-15? + ? + 5 GAS gp140 family IL-3 (myeloid) − − + − 5 GAS (IRF1 > IFP >>Ly6) IL-5 (myeloid) − − + − 5 GAS GM-CSF (myeloid) − − + − 5 GAS Growthhormone family GH ? − + − 5 PRL ? +/− + − 1, 3, 5 EPO ? − + − 5 GAS(B-CAS > IRF1 = IFP >> Ly6) Receptor Tyrosine Kinases EGF ? + + − 1, 3GAS (IRF1) PDGF ? + + − 1, 3 CSF-1 ? + + − 1, 3 GAS (not IRF1)

To construct a synthetic GAS containing promoter element, which is usedin the Biological Assays described in Examples 13-14, a PCR basedstrategy is employed to generate a GAS-SV40 promoter sequence. The 5′primer contains four tandem copies of the GAS binding site found in theIRF1 promoter and previously demonstrated to bind STATs upon inductionwith a range of cytokines (Rothman et al., Immunity 1:457-468 (1994).),although other GAS or ISRE elements can be used instead. The 5′ primeralso contains 18 bp of sequence complementary to the SV40 early promotersequence and is flanked with an XhoI site. The sequence of the 5′ primeris: (SEQ ID NO:3) 5′:GCGCCTCGAGATTTCCCCGAAATCTAGATTTCCCCGAAATGATTTCCCCGAAATGATTTCCCGGAAATATCTGCCATCTCAATTAG:3′

The downstream primer is complementary to the SV40 promoter and isflanked with a Hind III site: 5′:GCGGCAAGCTTTTTGCAAAGCCTAGGC:3′ (SEQ IDNO:4)

PCR amplification is performed using the SV40 promoter template presentin the B-gal:promoter plasmid obtained from Clontech. The resulting PCRfragment is digested with XhoI/Hind III and subcloned intoBLSK2-(Stratagene.) Sequencing with forward and reverse primers confirmsthat the insert contains the following sequence: (SEQ ID NO:5)5′:CTCGAGATTTCCCCGAAATCTAGATTTCCCCGAAATGATTTCCCCGAAATGATTTCCCCGAAATATCTGCCATCTCAATTAGTCAGCAACCATAGTCCCGCCCCTAACTCCGCCCATCCCGCCCCTAACTCCGCCCAGTTCCGCCCATTCTCCGCCCCATGGCTGACTAATTTTTTTTATTTATGCAGAGGCCGAGGCCGCCTCGGCCTCTGAGCTATTCCAGAAGTAGTGAGGAGGCTTTTTTGGAGGCCTAGGCTTTTGCAAAAAGCTT:3′

With this GAS promoter element linked to the SV40 promoter, a GAS:SEAP2reporter construct is next engineered. Here, the reporter molecule is asecreted alkaline phosphatase, or “SEAP.” Clearly, however, any reportermolecule can be instead of SEAP, in this or in any of the otherExamples. Well known reporter molecules that can be used instead of SEAPinclude chloramphenicol acetyltransferase (CAT), luciferase, alkalinephosphatase, B-galactosidase, green fluorescent protein (GFP), or anyprotein detectable by an antibody.

The above sequence confirmed synthetic GAS-SV40 promoter element issubcloned into the pSEAP-Promoter vector obtained from Clontech usingHindIlI and XhoI, effectively replacing the SV40 promoter with theamplified GAS:SV40 promoter element, to create the GAS-SEAP vector.However, this vector does not contain a neomycin resistance gene, andtherefore, is not preferred for mammalian expression systems.

Thus, in order to generate mammalian stable cell lines expressing theGAS-SEAP reporter, the GAS-SEAP cassette is removed from the GAS-SEAPvector using SalI and NotI, and inserted into a backbone vectorcontaining the neomycin resistance gene, such as pGFP-1 (Clontech),using these restriction sites in the multiple cloning site, to createthe GAS-SEAP/Neo vector. Once this vector is transfected into mammaliancells, this vector can then be used as a reporter molecule for GASbinding as described in Examples 13-14.

Other constructs can be made using the above description and replacingGAS with a different promoter sequence. For example, construction ofreporter molecules containing NFK-B and EGR promoter sequences aredescribed in Examples 15 and 16. However, many other promoters can besubstituted using the protocols described in these Examples. Forinstance, SRE, IL-2, NFAT, or Osteocalcin promoters can be substituted,alone or in combination (e.g., GAS/NF-KB/EGR, GAS/NF-KB, Il-2/NFAT, orNF-KB/GAS). Similarly, other cell lines can be used to test reporterconstruct activity, such as HELA (epithelial), HUVEC (endothelial), Reh(B-cell), Saos-2 (osteoblast), HUVAC (aortic), or Cardiomyocyte.

Example 13 High-Throughput Screening Assay for T-Cell Activity

The following protocol is used to assess T-cell activity by identifyingfactors, such as growth factors and cytokines, that may proliferate ordifferentiate T-cells. T-cell activity is assessed using theGAS/SEAP/Neo construct produced in Example 12. Thus, factors thatincrease SEAP activity indicate the ability to activate the Jaks-STATSsignal transduction pathway. The T-cell used in this assay is JurkatT-cells (ATCC Accession No. TIB-152), although Molt-3 cells (ATCCAccession No. CRL-1552) and Molt-4 cells (ATCC Accession No. CRL-1582)cells can also be used.

Jurkat T-cells are lymphoblastic CD4+ Th1 helper cells. In order togenerate stable cell lines, approximately 2 million Jurkat cells aretransfected with the GAS-SEAP/neo vector using DMRIE-C (LifeTechnologies) (transfection procedure described below). The transfectedcells are seeded to a density of approximately 20,000 cells per well andtransfectants resistant to 1 mg/ml genticin selected. Resistant coloniesare expanded and then tested for their response to increasingconcentrations of interferon gamma. The dose response of a selectedclone is demonstrated.

Specifically, the following protocol will yield sufficient cells for 75wells containing 200 ul of cells. Thus, it is either scaled up, orperformed in multiple to generate sufficient cells for multiple 96 wellplates. Jurkat cells are maintained in RPMI+10% serum with 1% Pen-Strep.Combine 2.5 mls of OPTI-MEM (Life Technologies) with 10 ug of plasmidDNA in a T25 flask. Add 2.5 ml OPTI-MEM containing 50 ul of DMRIE-C andincubate at room temperature for 15-45 mins.

During the incubation period, count cell concentration, spin down therequired number of cells (10⁷ per transfection), and resuspend inOPTI-MEM to a final concentration of 10⁷ cells/ml. Then add 1 ml of1×10⁷ cells in OPTI-MEM to T25 flask and incubate at 37° C. for 6 hrs.After the incubation, add 10 ml of RPMI+15% seru

The Jurkat: GAS-SEAP stable reporter lines are maintained in RPMI+10%serum, 1 mg/ml Genticin, and 1% Pen-Strep. These cells are treated withsupernatants containing a polypeptide as produced by the protocoldescribed in Example 11.

On the day of treatment with the supernatant, the cells should be washedand resuspended in fresh RPMI+10% serum to a density of 500,000 cellsper ml. The exact number of cells required will depend on the number ofsupernatants being screened. For one 96 well plate, approximately 10million cells (for 10 plates, 100 million cells) are required.

Transfer the cells to a triangular reservoir boat, in order to dispensethe cells into a 96 well dish, using a 12 channel pipette. Using a 12channel pipette, transfer 200 ul of cells into each well (thereforeadding 100, 000 cells per well).

After all the plates have been seeded, 50 ul of the supernatants aretransferred directly from the 96 well plate containing the supernatantsinto each well using a 12 channel pipette. In addition, a dose ofexogenous interferon gamma (0.1, 1.0, 10 ng) is added to wells H9, H10,and H11 to serve as additional positive controls for the assay.

The 96 well dishes containing Jurkat cells treated with supernatants areplaced in an incubator for 48 hrs (note: this time is variable between48-72 hrs). 35 ul samples from each well are then transferred to anopaque 96 well plate using a 12 channel pipette. The opaque platesshould be covered (using sellophene covers) and stored at −20° C. untilSEAP assays are performed according to Example 17. The plates containingthe remaining treated cells are placed at 4° C. and serve as a source ofmaterial for repeating the assay on a specific well if desired.

As a positive control, 100 Unit/ml interferon gamma can be used which isknown to activate Jurkat T cells. Over 30 fold induction is typicallyobserved in the positive control wells.

Example 14 High-Throughput Screening Assay Identifying Myeloid Activity

The following protocol is used to assess myeloid activity by identifyingfactors, such as growth factors and cytokines, that may proliferate ordifferentiate myeloid cells. Myeloid cell activity is assessed using theGAS/SEAP/Neo construct produced in Example 12. Thus, factors thatincrease SEAP activity indicate the ability to activate the Jaks-STATSsignal transduction pathway. The myeloid cell used in this assay isU937, a pre-monocyte cell line, although TF-1, HL60, or KG1 can be used.

To transiently transfect U937 cells with the GAS/SEAP/Neo constructproduced in Example 12, a DEAE-Dextran method (Kharbanda et. al., 1994,Cell Growth & Differentiation, 5:259-265) is used. First, harvest 2×10e⁷U937 cells and wash with PBS. The U937 cells are usually grown in RPMI1640 medium containing 10% beat-inactivated fetal bovine serum (FBS)supplemented with 100 units/ml penicillin and 100 mg/ml streptomycin.

Next, suspend the cells in 1 ml of 20 mM Tris-HCl (pH 7.4) buffercontaining 0.5 mg/ml DEAE-Dextran 8 ug GAS-SEAP2 plasmid DNA, 140 mMNaCl, 5 mM KCl, 375 uM Na₂HPO₄.7H₂O, 1 mM MgCl₂, and 675 uM CaCl₂.Incubate at 37° C. for 45 min.

Wash the cells with RPMI 1640 medium containing 10% FBS and thenresuspend in 10 ml complete medium and incubate at 37° C. for 36 hr.

The GAS-SEAP/U937 stable cells are obtained by growing the cells in 400ug/ml G418. The G418-free medium is used for routine growth but everyone to two months, the cells should be re-grown in 400 ug/ml G418 forcouple of passages.

These cells are tested by harvesting 1×10⁸ cells (this is enough for ten96-well plates assay) and wash with PBS. Suspend the cells in 200 mlabove described growth medium, with a final density of 5×10⁵ cells/ml.Plate 200 ul cells per well in the 96-well plate (or 1×10⁵ cells/well).

Add 50 ul of the supernatant prepared by the protocol described inExample 11. Incubate at 37° C. for 72 hr. As a positive control, 100Unit/ml interferon gamma can be used which is known to activate U937cells. Over 30 fold induction is typically observed in the positivecontrol wells. SEAP assay the supernatant according to the protocoldescribed in Example 17.

Example 15 High-Throughput Screening Assay Identifying Neuronal Activity

When cells undergo differentiation and proliferation, a group of genesare activated through many different signal transduction pathways. Oneof these genes, EGR1 (early growth response gene 1), is induced invarious tissues and cell types upon activation. The promoter of EGR1 isresponsible for such induction. Using the EGR1 promoter linked toreporter molecules, activation of cells can be assessed.

Particularly, the following protocol is used to assess neuronal activityin PC12 cell lines. PC12 cells (rat phenochromocytoma cells) are knownto proliferate and/or differentiate by activation with a number ofmitogens, such as TPA (tetradecanoyl phorbol acetate), NGF (nerve growthfactor), and EGF (epidermal growth factor). The EGR1 gene expression isactivated during this treatment. Thus, by stably transfecting PC12 cellswith a construct containing an EGR promoter linked to SEAP reporter,activation of PC12 cells can be assessed.

The EGR/SEAP reporter construct can be assembled by the followingprotocol. The EGR-1 promoter sequence (−633 to +1) (Sakamoto K et al.,Oncogene 6:867-871 (1991)) can be PCR amplified from human genomic DNAusing the following primers: (SEQ ID NO:6)5′ GCGCTCGAGGGATGACAGCGATAGAAGCCCGG-3′ (SEQ ID NO:7)5′ GCGAAGCTTCGCGACTCCCCGGATCCGCCTC-3′

Using the GAS:SEAP/Neo vector produced in Example 12, EGR1 amplifiedproduct can then be inserted into this vector. Linearize theGAS:SEAP/Neo vector using restriction enzymes XhoI/HindIII, removing theGAS/SV40 stuffer. Restrict the EGR1 amplified product with these sameenzymes. Ligate the vector and the EGR1 promoter.

To prepare 96 well-plates for cell culture, two mls of a coatingsolution (1:30 dilution of collagen type I (Upstate Biotech Inc.Cat#08-115) in 30% ethanol (filter sterilized)) is added per one 10 cmplate or 50 ml per well of the 96-well plate, and allowed to air dry for2 hr.

PC12 cells are routinely grown in RPMI-1640 medium (Bio Whittaker)containing 10% horse serum (JRH BIOSCIENCES, Cat. # 12449-78P), 5%heat-inactivated fetal bovine serum (FBS) supplemented with 100 units/mlpenicillin and 100 ug/ml streptomycin on a precoated 10 cm tissueculture dish. One to four split is done every three to four days. Cellsare removed from the plates by scraping and resuspended with pipettingup and down for more than 15 times.

Transfect the EGR/SEAP/Neo construct into PC12 using the Lipofectamineprotocol described in Example 11. EGR-SEAP/PC12 stable cells areobtained by growing the cells in 300 ug/ml G418. The G418-free medium isused for routine growth but every one to two months, the cells should bere-grown in 300 ug/ml G418 for couple of passages.

To assay for neuronal activity, a 10 cm plate with cells around 70 to80% confluent is screened by removi the old medium. Wash the cells oncewith PBS (Phosphate buffered saline). Then starve the cells in low serummedium (RPMI-1640 containing 1% horse serum and 0.5% FBS withantibiotics) overnight.

The next moming, remove the medium and wash the cells with PBS. Scrapeoff the cells from the plate, suspend the cells well in 2 ml low serummedium. Count the cell number and add more low serum medium to reachfinal cell density as 5×10⁵ cells/ml.

Add 200 ul of the cell suspension to each well of 96-well plate(equivalent to 1×10⁵ cells/well). Add 50 ul supernatant produced byExample 11, 37° C. for 48 to 72 hr. As a positive control, a growthfactor known to activate PC12 cells through EGR can be used, such as 50ng/ul of Neuronal Growth Factor (NGF). Over fifty-fold induction of SEAPis typically seen in the positive control wells. SEAP assay thesupernatant according to Example 17.

Example 16 High-Throughput Screening Assay for T-Cell Activity

NF-κB (Nuclear Factor κB) is a transcription factor activated by a widevariety of agents including the inflammatory cytokines IL-1 and TNF,CD30 and CD40, lymphotoxin-alpha and lymphotoxin-beta, by exposure toLPS or thrombin, and by expression of certain viral gene products. As atranscription factor, NF-κB regulates the expression of genes involvedin immune cell activation, control of apoptosis (NF-κB appears to shieldcells from apoptosis), B and T-cell development, anti-viral andantimicrobial responses, and multiple stress responses.

In non-stimulated conditions, NF-κB is retained in the cytoplasm withI-κB (Inhibitor κB). However, upon stimulation, I-κB is phosphorylatedand degraded, causing NF-κB to shuttle to the nucleus, therebyactivating transcription of target genes. Target genes activated byNF-κB include IL-2, IL-6, GM-CSF, ICAM-1 and class 1 MHC.

Due to its central role and ability to respond to a range of stimuli,reporter constructs utilizing the NF-κB promoter element are used toscreen the supernatants produced in Example 11. Activators or inhibitorsof NF-κB would be useful in treating diseases. For example, inhibitorsof NF-κB could be used to treat those diseases related to the acute orchronic activation of NF-κB, such as rheumatoid arthritis.

To construct a vector containing the NF-κB promoter element, a PCR basedstrategy is employed. The upstream primer contains four tandem copies ofthe NF-κB binding site (GGGGACTTTCCC) (SEQ ID NO:8), 18 bp of sequencecomplementary to the 5′ end of the SV40 early promoter sequence, and isflanked with an XhoI site: (SEQ ID NO:9)5′:GCGGCCTCGAGGGGACTTTCCCGGGGACTTTCCGGGGACTTTCCGGGACTTTCCATCCTGCCATCTCAATTAG:3′

The downstream primer is complementary to the 3′ end of the SV40promoter and is flanked with a Hind III site: (SEQ ID NO:4)5′:GCGGCAAGCTTTTTGCAAAGCCTAGGC:3′

PCR amplification is performed using the SV40 promoter template presentin the pB-gal:promoter plasmid obtained from Clontech. The resulting PCRfragment is digested with XhoI and Hind III and subcloned into BLSK2-.(Stratagene) Sequencing with the T7 and T3 primers confirms the insertcontains the following sequence: (SEQ ID NO:10)5′:CTCGAGGGGACTTTCCCGGGGACTTTCCGGGGACTTTCCGGGACTTTCCATCTGCCATCTCAATTAGTCAGCAACCATAGTCCCGCCCCTAACTCCGCCCATCCCGCCCCTAACTCCGCCCAGTTCCGCCCATTCTCCGCCCCATGGCTGACTAATTTTTTTTATTTATGCAGAGGCCGAGGCCGCCTCGGCCTCTGAGCTATTCCAGAAGTAGTGAGGAGGCTTTTTTGGAGGCCTAGGCTTTTGC AAAAAGCTT:3′.

Next, replace the SV40 minimal promoter element present in thepSEAP2-promoter plasmid (Clontech) with this NF-κB/SV40 fragment usingXhoI and HindIII. However, this vector does not contain a neomycinresistance gene, and therefore, is not preferred for mammalianexpression systems.

In order to generate stable mammalian cell lines, the NF-κB/SV40/SEAPcassette is removed from the above NF-κB/SEAP vector using restrictionenzymes SalI and NotI, and inserted into a vector containing neomycinresistance. Particularly, the NF-κB/SV40/SEAP cassette was inserted intopGFP-1 (Clontech), replacing the GFP gene, after restricting pGFP-1 withSalI and NotI.

Once NF-κB/SV40/SEAP/Neo vector is created, stable Jurkat T-cells arecreated and maintained according to the protocol described in Example13. Similarly, the method for assaying supernatants with these stableJurkat T-cells is also described in Example 13. As a positive control,exogenous TNF alpha (0.1, 1, 10 ng) is added to wells H9, H10, and H11,with a 5-10 fold activation typically observed.

Example 17 Assay for SEAP Activity

As a reporter molecule for the assays described in Examples 13-16, SEAPactivity is assayed using the Tropix Phospho-light Kit (Cat. BP-400)according to the following general procedure. The Tropix Phospho-lightKit supplies the Dilution, Assay, and Reaction Buffers used below.

Prime a dispenser with the 2.5× Dilution Buffer and dispense 15 μl of2.5× dilution buffer into Optiplates containing 35 μl of a supernatant.Seal the plates with a plastic sealer and incubate at 65° C. for 30 min.Separate the Optiplates to avoid uneven heating.

Cool the samples to room temperature for 15 minutes. Empty the dispenserand prime with the Assay Buffer. Add 50 μl Assay Buffer and incubate atroom temperature 5 min. Empty the dispenser and prime with the ReactionBuffer (see the table below). Add 50 μl Reaction Buffer and incubate atroom temperature for 20 minutes. Since the intensity of thechemiluminescent signal is time dependent, and it takes about 10 minutesto read 5 plates on luminometer, one should treat 5 plates at each timeand start the second set 10 minutes later.

Read the relative light unit in the luminometer. Set H12 as blank, andprint the results. An increase in chemiluminescence indicates reporteractivity.

Reaction Buffer Formulation: # of plates Rxn buffer diluent (ml) CSPD(ml) 10 60 3 11 65 3.25 12 70 3.5 13 75 3.75 14 80 4 15 85 4.25 16 904.5 17 95 4.75 18 100 5 19 105 5.25 20 110 5.5 21 115 5.75 22 120 6 23125 6.25 24 130 6.5 25 135 6.75 26 140 7 27 145 7.25 28 150 7.5 29 1557.75 30 160 8 31 165 8.25 32 170 8.5 33 175 8.75 34 180 9 35 185 9.25 36190 9.5 37 195 9.75 38 200 10 39 205 10.25 40 210 10.5 41 215 10.75 42220 11 43 225 11.25 44 230 11.5 45 235 11.75 46 240 12 47 245 12.25 48250 12.5 49 255 12.75 50 260 13

Example 18 High-Throughput Screening Assay Identifying Changes in SmallMolecule Concentration and Membrane Permeability

Binding of a ligand to a receptor is known to alter intracellular levelsof small molecules, such as calcium, potassium, sodium, and pH, as wellas alter membrane potential. These alterations can be measured in anassay to identify supernatants which bind to receptors of a particularcell. Although the following protocol describes an assay for calcium,this protocol can easily be modified to detect changes in potassium,sodium, pH, membrane potential, or any other small molecule which isdetectable by a fluorescent probe.

The following assay uses Fluorometric Imaging Plate Reader (“FLIPR”) tomeasure changes in fluorescent molecules (Molecular Probes) that bindsmall molecules. Clearly, any fluorescent molecule detecting a smallmolecule can be used instead of the calcium fluorescent molecule,fluo-3, used here.

For adherent cells, seed the cells at 10,000-20,000 cells/well in aCo-star black 96-well plate with clear bottom. The plate is incubated ina CO₂ incubator for 20 hours. The adherent cells are washed two times inBiotek washer with 200 ul of HBSS (Hank's Balanced Salt Solution)leaving 100 ul of buffer after the final wash.

A stock solution of 1 mg/ml fluo-3 is made in 10% pluronic acid DMSO. Toload the cells with fluo-3, 50 ul of 12 ug/ml fluo-3 is added to eachwell. The plate is incubated at 37° C. in a CO₂ incubator for 60 min.The is washed four times in the Biotek washer with HBSS leaving 100 ulof buffer.

For non-adherent cells, the cells are spun down from culture media.Cells are re-suspended to 2-5×10⁶ cells/ml with HBSS in a 50-ml conicaltube. 4 ul of 1 mg/ml fluo-3 solution in 10% pluronic acid DMSO is addedto each ml of cell suspension. The tube is then placed in a 37° C. waterbath for 30-60 min. The cells are washed twice with HBSS, resuspended to1×10⁶ cells/ml, and dispensed into a microplate, 100 ul/well. The plateis centrifuged at 1000 rpm for 5 min. The plate is then washed once inDenley CellWash with 200 ul, followed by an aspiration step to 100 ulfinal volume.

For a non-cell based assay, each well contains a fluorescent molecule,such as fluo-3. The supernatant is added to the well, and a change influorescence is detected.

To measure the fluorescence of intracellular calcium, the FLIPR is setfor the following parameters: (1) System gain is 300-800 mW; (2)Exposure time is 0.4 second; (3) Camera F/stop is F/2; (4) Excitation is488 nm; (5) Emission is 530 nm; and (6) Sample addition is 50 ul.Increased emission at 530 nm indicates an extracellular signaling eventwhich has resulted in an increase in the intracellular Ca⁺⁺concentration.

Example 19 High-Throughput Screening Assay Identifying Tyrosine KinaseActivity

The Protein Tyrosine Kinases (PTK) represent a diverse group oftransmembrane and cytoplasmic kinases. Within the Receptor ProteinTyrosine Kinase RPTK) group are receptors for a range of mitogenic andmetabolic growth factors including the PDGF, FGF, EGF, NGF, HGF andInsulin receptor subfamilies. In addition there are a large family ofRPTKs for which the corresponding ligand is unknown. Ligands for RPTKsinclude mainly secreted small proteins, but also membrane-bound andextracellular matrix proteins.

Activation of RPTK by ligands involves ligand-mediated receptordimerization, resulting in transphosphorylation of the receptor subunitsand activation of the cytoplasmic tyrosine kinases. The cytoplasmictyrosine kinases include receptor associated tyrosine kinases of thesrc-family (e.g., src, yes, lck, lyn, fyn) and non-receptor linked andcytosolic protein tyrosine kinases, such as the Jak family, members ofwhich mediate signal transduction triggered by the cytokine superfamilyof receptors (e.g., the Interleukins, Interferons, GM-CSF, and Leptin).

Because of the wide range of known factors capable of stimulatingtyrosine kinase activity, the identification of novel human secretedproteins capable of activating tyrosine kinase signal transductionpathways are of interest. Therefore, the following protocol is designedto identify those novel human secreted proteins capable of activatingthe tyrosine kinase signal transduction pathways.

Seed target cells (e.g., primary keratinocytes) at a density ofapproximately 25,000 cells per well in a 96 well Loprodyne Silent ScreenPlates purchased from Nalge Nunc (Naperville, Ill.). The plates aresterilized with two 30 minute rinses with 100% ethanol, rinsed withwater and dried overnight. Some plates are coated for 2 hr with 100 mlof cell culture grade type I collagen (50 mg/ml), gelatin (2%) orpolylysine (50 mg/ml), all of which can be purchased from SigmaChemicals (St. Louis, Mo.) or 10% Matrigel purchased from BectonDickinson (Bedford, Mass.), or calf serum, rinsed with PBS and stored at4° C. Cell growth on these plates is assayed by seeding 5,000 cells/wellin growth medium and indirect quantitation of cell number through use ofalamarBlue as described by the manufacturer Alamar Biosciences, Inc.(Sacramento, Calif.) after 48 hr. Falcon plate covers #3071 from BectonDickinson (Bedford, Mass.) are used to cover the Loprodyne Silent ScreenPlates. Falcon Microtest III cell culture plates can also be used insome proliferation experiments.

To prepare extracts, A431 cells are seeded onto the nylon membranes ofLoprodyne plates (20,000/200 ml/well) and cultured overnight in completemedium. Cells are quiesced by incubation in serum-free basal medium for24 hr. After 5-20 minutes treatment with EGF (60 ng/ml) or 50 ul of thesupernatant produced in Example 11, the medium was removed and 100 ml ofextraction buffer ((20 mM HEPES pH 7.5, 0.15 M NaCl, 1% Triton X-100,0.1% SDS, 2 mM Na3VO4, 2 mM Na4P2O7 and a cocktail of proteaseinhibitors (# 1836170) obtained from Boeheringer Mannheim (Indianapolis,Ind.) is added to each well and the plate is shaken on a rotating shakerfor 5 minutes at 4° C. The plate is then placed in a vacuum transfermanifold and the extract filtered through the 0.45 mm membrane bottomsof each well using house vacuum. Extracts are collected in a 96-wellcatch/assay plate in the bottom of the vacuum manifold and immediatelyplaced on ice. To obtain extracts clarified by centrifugation, thecontent of each well, after detergent solubilization for 5 minutes, isremoved and centrifuged for 15 minutes at 4° C. at 16,000×g.

Test the filtered extracts for levels of tyrosine kinase activity.Although many methods of detecting tyrosine kinase activity are known,one method is described here.

Generally, the tyrosine kinase activity of a supernatant is evaluated bydetermining its ability to phosphorylate a tyrosine residue on aspecific substrate (a biotinylated peptide). Biotinylated peptides thatcan be used for this purpose include PSK1 (corresponding to amino acids6-20 of the cell division kinase cdc2-p34) and PSK2 (corresponding toamino acids 1-17 of gastrin). Both peptides are substrates for a rangeof tyrosine kinases and are available from Boehringer Mannheim.

The tyrosine kinase reaction is set up by adding the followingcomponents in order. First, add 10 ul of 5 uM Biotinylated Peptide, then10 ul ATP/Mg₂₊ (5 mM ATP/50 mM MgCl₂), then 10 ul of 5× Assay Buffer (40mM imidazole hydrochloride, pH7.3, 40 mM beta-glycerophosphate, 1 mMEGTA, 100 mM MgCl₂, 5 mM MnCl₂, 0.5 mg/ml BSA), then 5 ul of SodiumVanadate (1 mM), and then 5 ul of water. Mix the components gently andpreincubate the reaction mix at 30° C. for 2 min. Initial the reactionby adding 10 ul of the control enzyme or the filtered supernatant.

The tyrosine kinase assay reaction is then terminated by adding 10 ul of120 mm EDTA and place the reactions on ice.

Tyrosine kinase activity is determined by transferring 50 ul aliquot ofreaction mixture to a microtiter plate (MTP) module and incubating at37° C. for 20 min. This allows the streptavadin coated 96 well plate toassociate with the biotinylated peptide. Wash the MTP module with 300ul/well of PBS four times. Next add 75 ul of anti-phospotyrosineantibody conjugated to horse radish peroxidase(anti-P-Tyr-POD(0.5 u/ml))to each well and incubate at 37° C. for one hour. Wash the well asabove.

Next add 100 ul of peroxidase substrate solution (Boehringer Mannheim)and incubate at room temperature for at least 5 mins (up to 30 min).Measure the absorbance of the sample at 405 nm by using ELISA reader.The level of bound peroxidase activity is quantitated using an ELISAreader and reflects the level of tyrosine kinase activity.

Example 20 High-Throughput Screening Assay Identifying PhosphorylationActivity

As a potential alternative and/or compliment to the assay of proteintyrosine kinase activity described in Example 19, an assay which detectsactivation (phosphorylation) of major intracellular signal transductionintermediates can also be used. For example, as described below oneparticular assay can detect tyrosine phosphorylation of the Erk-1 andErk-2 kinases. However, phosphorylation of other molecules, such as Raf,JNK, p38 MAP, Map kinase kinase (MEK), MEK kinase, Src, Muscle specifickinase (MuSK), IRAK, Tec, and Janus, as well as any other phosphoserine,phosphotyrosine, or phosphothreonine molecule, can be detected bysubstituting these molecules for Erk-1 or Erk-2 in the following assay.

Specifically, assay plates are made by coating the wells of a 96-wellELISA plate with 0.1 ml of protein G (1 ug/ml) for 2 hr at room temp,(RT). The plates are then rinsed with PBS and blocked with 3% BSA/PBSfor 1 hr at RT. The protein G plates are then treated with 2 commercialmonoclonal antibodies (10 ng/well) against Erk-1 and Erk-2 (1 hr at RT)(Santa Cruz Biotechnology). (To detect other molecules, this step caneasily be modified by substituting a monoclonal antibody detecting anyof the above described molecules.) After 3-5 rinses with PBS, the platesare stored at 4° C. until use.

A431 cells are seeded at 20,000/well in a 96-well Loprodyne filterplateand cultured overnight in growth medium. The cells are then starved for48 hr in basal medium (DMEM) and then treated with EGF (6 ng/well) or 50ul of the supernatants obtained in Example 11 for 5-20 minutes. Thecells are then solubilized and extracts filtered directly into the assayplate.

After incubation with the extract for 1 hr at RT, the wells are againrinsed. As a positive control, a commercial preparation of MAP kinase(10 ng/well) is used in place of A431 extract. Plates are then treatedwith a commercial polyclonal (rabbit) antibody (1 ug/ml) whichspecifically recognizes the phosphorylated epitope of the Erk-1 andErk-2 kinases (1 hr at RT). This antibody is biotinylated by standardprocedures. The bound polyclonal antibody is then quantitated bysuccessive incubations with Europium-streptavidin and Europiumfluorescence enhancing reagent in the Wallac DELFIA instrument(time-resolved fluorescence). An increased fluorescent signal overbackground indicates a phosphorylation.

Example 21 Method of Determining Alterations in a Gene Corresponding toa Polynucleotide

RNA isolated from entire families or individual patients presenting witha phenotype of interest (such as a disease) is be isolated. cDNA is thengenerated from these RNA samples using protocols known in the art. (See,Sambrook.) The cDNA is then used as a template for PCR, employingprimers surrounding regions of interest in SEQ ID NO:X. Suggested PCRconditions consist of 35 cycles at 95° C. for 30 seconds; 60-120 secondsat 52-58° C.; and 60-120 seconds at 70° C., using buffer solutionsdescribed in Sidransky, D., et al., Science 252:706 (1991).

PCR products are then sequenced using primers labeled at their 5′ endwith T4 polynucleotide kinase, employing SequiTherm Polymerase.(Epicentre Technologies). The intron-exon borders of selected exons isalso determined and genomic PCR products analyzed to confirm theresults. PCR products harboring suspected mutations is then cloned andsequenced to validate the results of the direct sequencing.

PCR products is cloned into T-tailed vectors as described in Holton, T.A. and Graham, M. W., Nucleic Acids Research, 19:1156 (1991) andsequenced with T7 polymerase (United States Biochemical). Affectedindividuals are identified by mutations not present in unaffectedindividuals.

Genomic rearrangements are also observed as a method of determiningalterations in a gene corresponding to a polynucleotide. Genomic clonesisolated according to Example 2 are nick-translated withdigoxigenindeoxy-uridine 5′-triphosphate (Boehringer Manheim), and FISHperformed as described in Johnson, Cg. et al., Methods Cell Biol.35:73-99 (1991). Hybridization with the labeled probe is carried outusing a vast excess of human cot-1 DNA for specific hybridization to thecorresponding genomic locus.

Chromosomes are counterstained with 4,6-diamino-2-phenylidole andpropidium iodide, producing a combination of C- and R-bands. Alignedimages for precise mapping are obtained using a triple-band filter set(Chroma Technology, Brattleboro, Vt.) in combination with a cooledcharge-coupled device camera (Photometrics, Tucson, Ariz.) and variableexcitation wavelength filters. (Johnson, Cv. et al., Genet. Anal. Tech.Appl., 8:75 (1991).) Image collection, analysis and chromosomalfractional length measurements are performed using the ISee GraphicalProgram System. (Inovision Corporation, Durham, N.C.) Chromosomealterations of the genomic region hybridized by the probe are identifiedas insertions, deletions, and translocations. These alterations are usedas a diagnostic marker for an associated disease.

Example 22 Method of Detecting Abnormal Levels of a Polypeptide in aBiological Sample

A polypeptide of the present invention can be detected in a biologicalsample, and if an increased or decreased level of the polypeptide isdetected, this polypeptide is a marker for a particular phenotype.Methods of detection are numerous, and thus, it is understood that oneskilled in the art can modify the following assay to fit theirparticular needs.

For example, antibody-sandwich ELISAs are used to detect polypeptides ina sample, preferably a biological sample. Wells of a microtiter plateare coated with specific antibodies, at a final concentration of 0.2 to10 ug/ml. The antibodies are either monoclonal or polyclonal and areproduced by the method described in Example 10. The wells are blocked sothat non-specific binding of the polypeptide to the well is reduced.

The coated wells are then incubated for >2 hours at RT with a samplecontaining the polypeptide. Preferably, serial dilutions of the sampleshould be used to validate results. The plates are then washed threetimes with deionized or distilled water to remove unbounded polypeptide.

Next, 50 ul of specific antibody-alkaline phosphatase conjugate, at aconcentration of 25-400 ng, is added and incubated for 2 hours at roomtemperature. The plates are again washed three times with deionized ordistilled water to remove unbounded conjugate.

Add 75 ul of 4-methylumbelliferyl phosphate (MUP) or p-nitrophenylphosphate (NPP) substrate solution to each well and incubate 1 hour atroom temperature. Measure the reaction by a microtiter plate reader.Prepare a standard curve, using serial dilutions of a control sample,and plot polypeptide concentration on the X-axis (log scale) andfluorescence or absorbance of the Y-axis (linear scale). Interpolate theconcentration of the polypeptide in the sample using the standard curve.

Example 23 Formulating a Polypeptide

The secreted polypeptide composition will be formulated and dosed in afashion consistent with good medical practice, taking into account theclinical condition of the individual patient (especially the sideeffects of treatment with the secreted polypeptide alone), the site ofdelivery, the method of administration, the scheduling ofadministration, and other factors known to practitioners. The “effectiveamount” for purposes herein is thus determined by such considerations.

As a general proposition, the total pharmaceutically effective amount ofsecreted polypeptide administered parenterally per dose will be in therange of about 1 μg/kg/day to 10 mg/kg/day of patient body weight,although, as noted above, this will be subject to therapeuticdiscretion. More preferably, this dose is at least 0.01 mg/kg/day, andmost preferably for humans between about 0.01 and 1 mg/kg/day for thehormone. If given continuously, the secreted polypeptide is typicallyadministered at a dose rate of about 1 μg/kg/hour to about 50μg/kg/hour, either by 1-4 injections per day or by continuoussubcutaneous infusions, for example, using a mini-pump. An intravenousbag solution may also be employed. The length of treatment needed toobserve changes and the interval following treatment for responses tooccur appears to vary depending on the desired effect.

Pharmaceutical compositions containing the secreted protein of theinvention are administered orally, rectally, parenterally,intracistemally, intravaginally, intraperitoneally, topically (as bypowders, ointments, gels, drops or transdermal patch), bucally, or as anoral or nasal spray. “Pharmaceutically acceptable carrier” refers to anon-toxic solid, semisolid or liquid filler, diluent, encapsulatingmaterial or formulation auxiliary of any type. The term “parenteral” asused herein refers to modes of administration which include intravenous,intramuscular, intraperitoneal, intrasternal, subcutaneous andintraarticular injection and infusion.

The secreted polypeptide is also suitably administered bysustained-release systems. Suitable examples of sustained-releasecompositions include semi-permeable polymer matrices in the form ofshaped articles, e.g., films, or mirocapsules. Sustained-releasematrices include polylactides (U.S. Pat. No. 3,773,919, EP 58,481),copolymers of L-glutamic acid and gamma-ethyl-L-glutamate (Sidman, U. etal., Biopolymers 22:547-556 (1983)), poly (2-hydroxyethyl methacrylate)(R. Langer et al., J. Biomed. Mater. Res. 15:167-277 (1981), and R.Langer, Chem. Tech. 12:98-105 (1982)), ethylene vinyl acetate (R. Langeret al.) or poly-D-(−)-3-hydroxybutyric acid (EP 133,988).Sustained-release compositions also include liposomally entrappedpolypeptides. Liposomes containing the secreted polypeptide are preparedby methods known per se: DE 3,218,121; Epstein et al., Proc. Natl. Acad.Sci. USA 82:3688-3692 (1985); Hwang et al., Proc. Natl. Acad. Sci. USA77:4030-4034 (1980); EP 52,322; EP 36,676; EP 88,046; EP 143,949; EP142,641; Japanese Pat. Appl. 83-118008; U.S. Pat. Nos. 4,485,045 and4,544,545; and EP 102,324. Ordinarily, the liposomes are of the small(about 200-800 Angstroms) unilamellar type in which the lipid content isgreater than about 30 mol. percent cholesterol, the selected proportionbeing adjusted for the optimal secreted polypeptide therapy.

For parenteral administration, in one embodiment, the secretedpolypeptide is formulated generally by mixing it at the desired degreeof purity, in a unit dosage injectable form (solution, suspension, oremulsion), with a pharmaceutically acceptable carrier, i.e., one that isnon-toxic to recipients at the dosages and concentrations employed andis compatible with other ingredients of the formulation. For example,the formulation preferably does not include oxidizing agents and othercompounds that are known to be deleterious to polypeptides.

Generally, the formulations are prepared by contacting the polypeptideuniformly and intimately with liquid carriers or finely divided solidcarriers or both. Then, if necessary, the product is shaped into thedesired formulation. Preferably the carrier is a parenteral carrier,more preferably a solution that is isotonic with the blood of therecipient. Examples of such carrier vehicles include water, saline,Ringer's solution, and dextrose solution. Non-aqueous vehicles such asfixed oils and ethyl oleate are also useful herein, as well asliposomes.

The carrier suitably contains minor amounts of additives such assubstances that enhance isotonicity and chemical stability. Suchmaterials are non-toxic to recipients at the dosages and concentrationsemployed, and include buffers such as phosphate, citrate, succinate,acetic acid, and other organic acids or their salts; antioxidants suchas ascorbic acid; low molecular weight (less than about ten residues)polypeptides, e.g., polyarginie or tripeptides; proteins, such as serumalbumin, gelatin, or immunoglobulins; hydrophilic polymers such aspolyvinylpyrrolidone; amino acids, such as glycine, glutamic acid,aspartic acid, or arginine; monosaccharides, disaccharides, and othercarbohydrates including cellulose or its derivatives, glucose, manose,or dextrins; chelating agents such as EDTA; sugar alcohols such asmannitol or sorbitol; counterions such as sodium; and/or nonionicsurfactants such as polysorbates, poloxamers, or PEG.

The secreted polypeptide is typically formulated in such vehicles at aconcentration of about 0.1 mg/ml to 100 mg/ml, preferably 1-10 mg/ml, ata pH of about 3 to 8. It will be understood that the use of certain ofthe foregoing excipients, carriers, or stabilizers will result in theformation of polypeptide salts.

Any polypeptide to be used for therapeutic administration can besterile. Sterility is readily accomplished by filtration through sterilefiltration membranes (e.g., 0.2 micron membranes). Therapeuticpolypeptide compositions generally are placed into a container having asterile access port, for example, an intravenous solution bag or vialhaving a stopper pierceable by a hypodermic injection needle.

Polypeptides ordinarily will be stored in unit or multi-dose containers,for example, sealed ampoules or vials, as an aqueous solution or as alyophilized formulation for reconstitution. As an example of alyophilized formulation, 10-ml vials are filled with 5 ml ofsterile-filtered 1% (w/v) aqueous polypeptide solution, and theresulting mixture is lyophilized. The infusion solution is prepared byreconstituting the lyophilized polypeptide using bacteriostaticWater-for-Injection.

The invention also provides a pharmaceutical pack or kit comprising oneor more containers filled with one or more of the ingredients of thepharmaceutical compositions of the invention. Associated with suchcontainer(s) can be a notice in the form prescribed by a governmentalagency regulating the manufacture, use or sale of pharmaceuticals orbiological products, which notice reflects approval by the agency ofmanufacture, use or sale for human administration. In addition, thepolypeptides of the present invention may be employed in conjunctionwith other therapeutic compounds.

Example 24 Method of Treating Decreased Levels of the Polypeptide

It will be appreciated that conditions caused by a decrease in thestandard or normal expression level of a secreted protein in anindividual can be treated by administering the polypeptide of thepresent invention, preferably in the secreted form. Thus, the inventionalso provides a method of treatment of an individual in need of anincreased level of the polypeptide comprising administering to such anindividual a pharmaceutical composition comprising an amount of thepolypeptide to increase the activity level of the polypeptide in such anindividual.

For example, a patient with decreased levels of a polypeptide receives adaily dose 0.1-100 ug/kg of the polypeptide for six consecutive days.Preferably, the polypeptide is in the secreted form. The exact detailsof the dosing scheme, based on administration and formulation, areprovided in Example 23.

Example 25 Method of Treating Increased Levels of the Polypeptide

Antisense technology is used to inhibit production of a polypeptide ofthe present invention. This technology is one example of a method ofdecreasing levels of a polypeptide, preferably a secreted form, due to avariety of etiologies, such as cancer.

For example, a patient diagnosed with abnormally increased levels of apolypeptide is administered intravenously antisense polynucleotides at0.5, 1.0, 1.5, 2.0 and 3.0 mg/kg day for 21 days. This treatment isrepeated after a 7-day rest period if the treatment was well tolerated.The formulation of the antisense polynucleotide is provided in Example23.

Example 26 Method of Treatment Using Gene Therapy

One method of gene therapy transplants fibroblasts, which are capable ofexpressing a polypeptide, onto a patient. Generally, fibroblasts areobtained from a subject by skin biopsy. The resulting tissue is placedin tissue-culture medium and separated into small pieces. Small chunksof the tissue are placed on a wet surface of a tissue culture flask,approximately ten pieces are placed in each flask. The flask is turnedupside down, closed tight and left at room temperature over night. After24 hours at room temperature, the flask is inverted and the chunks oftissue remain fixed to the bottom of the flask and fresh media (e.g.,Ham's F12 media, with 10% FBS, penicillin and streptomycin) is added.The flasks are then incubated at 37° C. for approximately one week.

At this time, fresh media is added and subsequently changed everyseveral days. After an additional two weeks in culture, a monolayer offibroblasts emerge. The monolayer is trypsinized and scaled into largerflasks.

pMV-7 (Kirschmeier, P. T. et al., DNA, 7:219-25 (1988)), flanked by thelong terminal repeats of the Moloney murine sarcoma virus, is digestedwith EcoRI and HindIII and subsequently treated with calf intestinalphosphatase. The linear vector is fractionated on agarose gel andpurified, using glass beads.

The cDNA encoding a polypeptide of the present invention can beamplified using PCR primers which correspond to the 5′ and 3′ endsequences respectively as set forth in Example 1. Preferably, the 5′primer contains an EcoRI site and the 3′ primer includes a HindIII site.Equal quantities of the Moloney murine sarcoma virus linear backbone andthe amplified EcoRI and HindHIII fragment are added together, in thepresence of T4 DNA ligase. The resulting mixture is maintained underconditions appropriate for ligation of the two fragments. The ligationmixture is then used to transform bacteria HB101, which are then platedonto agar containing kanamycin for the purpose of confirming that thevector has the gene of interest properly inserted.

The amphotropic pA317 or GP+am12 packaging cells are grown in tissueculture to confluent density in Dulbecco's Modified Eagles Medium (DMEM)with 10% calf serum (CS), penicillin and streptomycin. The MSV vectorcontaining the gene is then added to the media and the packaging cellstransduced with the vector. The packaging cells now produce infectiousviral particles containing the gene (the packaging cells are nowreferred to as producer cells).

Fresh media is added to the transduced producer cells, and subsequently,the media is harvested from a 10 cm plate of confluent producer cells.The spent media, containing the infectious viral particles, is filteredthrough a millipore filter to remove detached producer cells and thismedia is then used to infect fibroblast cells. Media is removed from asub-confluent plate of fibroblasts and quickly replaced with the mediafrom the producer cells. This media is removed and replaced with freshmedia. If the titer of virus is high, then virtually all fibroblastswill be infected and no selection is required. If the titer is very low,then it is necessary to use a retroviral vector that has a selectablemarker, such as neo or his. Once the fibroblasts have been efficientlyinfected, the fibroblasts are analyzed to determine whether protein isproduced.

The engineered fibroblasts are then transplanted onto the host, eitheralone or after having been grown to confluence on cytodex 3 microcarrierbeads.

It will be clear that the invention may be practiced otherwise than asparticularly described in the foregoing description and examples.Numerous modifications and variations of the present invention arepossible in light of the above teachings and, therefore, are within thescope of the appended claims.

The entire disclosure of each document cited (including patents, patentapplications, journal articles, abstracts, laboratory manuals, books, orother disclosures) in the Background of the Invention, DetailedDescription, and Examples is hereby incorporated herein by reference.Further, the hard copy of the sequence listing submitted herewith andthe corresponding computer readable form are both incorporated herein byreference in their entireties.

1. An isolated nucleic acid molecule comprising a polynucleotide havinga nucleotide sequence at least 95% identical to a sequence selected fromthe group consisting of: (a) a polynucleotide fragment of SEQ ID NO:X ora polynucleotide fragment of the cDNA sequence included in ATCC DepositNo: Z, which is hybridizable to SEQ ID NO:X; (b) a polynucleotideencoding a polypeptide fragment of SEQ ID NO:Y or a polypeptide fragmentencoded by the cDNA sequence included in ATCC Deposit No: Z, which ishybridizable to SEQ ID NO:X; (c) a polynucleotide encoding a polypeptidedomain of SEQ ID NO:Y or a polypeptide domain encoded by the cDNAsequence included in ATCC Deposit No: Z, which is hybridizable to SEQ IDNO:X; (d) a polynucleotide encoding a polypeptide epitope of SEQ ID NO:Yor a polypeptide epitope encoded by the cDNA sequence included in ATCCDeposit No: Z, which is hybridizable to SEQ ID NO:X; (e) apolynucleotide encoding a polypeptide of SEQ ID NO:Y or the cDNAsequence included in ATCC Deposit No: Z, which is hybridizable to SEQ IDNO:X, having biological activity; (f) a polynucleotide which is avariant of SEQ ID NO:X; (g) a polynucleotide which is an allelic variantof SEQ ID NO:X; (h) a polynucleotide which encodes a species homologueof the SEQ ID NO:Y; (i) a polynucleotide capable of hybridizing understringent conditions to any one of the polynucleotides specified in(a)-(h), wherein said polynucleotide does not hybridize under stringentconditions to a nucleic acid molecule having a nucleotide sequence ofonly A residues or of only T residues.
 2. The isolated nucleic acidmolecule of claim 1, wherein the polynucleotide fragment comprises anucleotide sequence encoding a secreted protein.
 3. The isolated nucleicacid molecule of claim 1, wherein the polynucleotide fragment comprisesa nucleotide sequence encoding the sequence identified as SEQ ID NO:Y orthe polypeptide encoded by the cDNA sequence included in ATCC DepositNo: Z, which is hybridizable to SEQ ID NO:X.
 4. The isolated nucleicacid molecule of claim 1, wherein the polynucleotide fragment comprisesthe entire nucleotide sequence of SEQ ID NO:X or the cDNA sequenceincluded in ATCC Deposit No: Z, which is hybridizable to SEQ ID NO:X. 5.A recombinant vector comprising the isolated nucleic acid molecule ofclaim
 1. 6. A method of making a recombinant host cell comprising theisolated nucleic acid molecule of claim
 1. 7. A recombinant host cellproduced by the method of claim
 6. 8. The recombinant host cell of claim7 comprising vector sequences.
 9. An isolated polypeptide comprising anamino acid sequence at least 95% identical to a sequence selected fromthe group consisting of: (a) a polypeptide fragment of SEQ ID NO:Y orthe encoded sequence included in ATCC Deposit No: Z; (b) a polypeptidefragment of SEQ ID NO:Y or the encoded sequence included in ATCC DepositNo: Z, having biological activity; (c) a polypeptide domain of SEQ IDNO:Y or the encoded sequence included in ATCC Deposit No: Z; (d) apolypeptide epitope of SEQ ID NO:Y or the encoded sequence included inATCC Deposit No: Z; (e) a secreted form of SEQ ID NO:Y or the encodedsequence included in ATCC Deposit No: Z; (f) a full length protein ofSEQ ID NO:Y or the encoded sequence included in ATCC Deposit No: Z; (g)a variant of SEQ ID NO:Y; (h) an allelic variant of SEQ ID NO:Y; or (i)a species homologue of the SEQ ID NO:Y.
 10. The isolated polypeptide ofclaim 9, wherein the secreted form or the full length protein comprisessequential amino acid deletions from either the C-terminus or theN-terminus.
 11. An isolated antibody that binds specifically to theisolated polypeptide of claim
 9. 12. A recombinant host cell thatexpresses the isolated polypeptide of claim
 9. 13. A method of making anisolated polypeptide comprising: (a) culturing the recombinant host cellof claim 7 under conditions such that said polypeptide is expressed; and(b) recovering said polypeptide.
 14. The polypeptide produced by claim13.
 15. A method for preventing, treating, or ameliorating a medicalcondition, comprising administering to a mammalian subject atherapeutically effective amount of the polynucleotide of claim
 1. 16. Amethod for preventing, treating, or ameliorating a medical condition,comprising administering to a mammalian subject a therapeuticallyeffective amount of the polypeptide of claim
 9. 17. A method forpreventing, treating, or ameliorating a medical condition, comprisingadministering to a mammalian subject a therapeutically effective amountof the antibody of claim
 11. 18. A method of diagnosing a pathologicalcondition or a susceptibility to a pathological condition in a subjectcomprising: (a) determining the presence or absence of a mutation in thepolynucleotide of claim 1; and (b) diagnosing a pathological conditionor a susceptibility to a pathological condition based on the presence orabsence of said mutation.
 19. A method of diagnosing a pathologicalcondition or a susceptibility to a pathological condition in a subjectcomprising: (a) determining the presence or amount of expression of thepolypeptide of claim 9 in a biological sample; and (b) diagnosing apathological condition or a susceptibility to a pathological conditionbased on the presence or amount of expression of the polypeptide.
 20. Amethod for identifying a binding partner to the polypeptide of claim 9comprising: (a) contacting the polypeptide of claim 9 with a bindingpartner; and (b) determining whether the binding partner effects anactivity of the polypeptide.